This bibliography of diamond
mechanosynthesis is an updated, expanded and annotated version
of a similar earlier bibliography that was first assembled by Freitas
on 16 December 2003 and posted
online at the Foresight Institute website. It now includes references
to mechanosynthetic fabrication employing the broader range of diamondoid
materials.

K.
Eric Drexler, “Molecular
engineering: an approach to the development of general capabilities
for molecular manipulation,” Proc. Natl. Acad. Sci.
(USA) 78(September 1981):5275-5278.ABSTRACT.
Development of the ability to design protein molecules will open a
path to the fabrication of devices to complex atomic specifications,
thus sidestepping obstacles facing conventional microtechnology. This
path will involve construction of molecular machinery able to position
reactive groups to atomic precision. It could lead to great advances
in computational devices and to the ability to manipulate biological
materials. The existence of this path has implications for the present.

H.H.
Farrell, M. Levinson, “Scanning
tunneling microscope as a structure-modifying tool,” Phys.
Rev. B 31(March 1985):3593-3598; http://prola.aps.org/abstract/PRB/v31/i6/p3593_1
(abstract)ABSTRACT.
We explore the possibility that surface charge induced by the scanning
tunneling microscope will influence the structure of the surface under
investigation. In general, we find that the emission currents limit
the induced charge densities and preclude major structural modifications
on the more stable surfaces. However, the possibility of modifying
less stable structures or of reducing the transition temperatures
for transformation between different surface phases does exist and
is discussed in detail.

Robert
Gomer, “Possible mechanisms
of atom transfer in scanning tunneling microscopy,” IBM
J. Res. Dev. 30(July 1986):428-430; http://www.research.ibm.com/journal/rd/304/ibmrd3004L.pdfABSTRACT.
Various mechanisms for the sudden transfer of an atom from or to the
tip of a scanning tunneling microscope are considered. It is concluded
that thermal desorption could be responsible and also that quasi-contact
in which the adsorbed atom is in effect "touching" both
surfaces, which would still be separated from each other by 2–4
Å, can lead to unactivated transfer via tunneling. For barrier
widths as small as 0.5 Å, however, tunneling becomes negligible.

K.
Eric Drexler, John S. Foster, “Synthetic
tips,” Nature 343(15 February 1990):600.EXTRACT.
Capabilities in scanning tunneling and atomic force microscopy (STM
and AFM) depend on probe-tip properties, but tip properties are at
present poorly controlled; suitable tips have poor reproducibility
at the atomic level. Techniques for precise control of the mechanical
and chemical nature of tip structures would be of evident value. We
therefore propose a ‘molecular tip’ made of a protein-like
molecule which has been designed to bind to a crystal-corner STM/AFM
tip, and which could potentially be tailored, manufactured and reproducible....Strong
and adjustable positional control of effective concentration (and
hence of reaction rates) on an atomic distance scale appears physically
possible in a class of systems that may be practically realizable.

K.
Eric Drexler, “Molecular
tip arrays for molecular imaging and nanofabrication,” J.
Vac. Sci. Technol. B 9(March 1991):1394-1397; http://link.aip.org/link/?JVTBD9/9/1394/1
(abstract)ABSTRACT.
A class of devices based on the atomic force microscope [Phys. Rev.
Lett. 56, 930 (1986)] is proposed that would enable
imaging with tips of atomically defined structure. These molecular
tip array (MTA) systems would enable sequential application of tips
with differing structures to a single sample, limited to a small substrate
area. MTAs with suitable binding sites can enable nanofabrication
via positional chemical synthesis exploiting local effective concentration
enhancements of ~108. A method for canceling
or inverting the net van der Waals attraction between a tip and a
substrate in a fluid medium is suggested, and a new analysis
of imaging forces for proteins is presented.

Ralph
C. Merkle, “Molecular
manufacturing: adding positional control to chemical synthesis,”
Chem. Design Automation News 8(September-October
1993):1;http://www.zyvex.com/nanotech/CDAarticle.htmlABSTRACT.
The long term goal of molecular manufacturing is to build exactly
what we want at low cost. Many if not most of the things that we'll
want to build are complex (like a molecular Cray computer), and seem
difficult if not impossible to synthesize with currently available
methods. Adding programmed positional control to the existing methods
used in synthesis should let us make a truly broad range of macroscopic
molecular structures. To add this kind of positional control, however,
requires that we design and build what amount to very small robotic
manipulators. If we are to make anything of any significant size with
this approach, we'll need mole quantities of these manipulators. Fortunately,
any truly general purpose manufacturing device should be able to manufacture
another general purpose manufacturing device, which lets us build
large numbers of such devices at low cost. This general approach,
used by trees for a very long time, should let us develop a low cost
general purpose molecular manufacturing technology. While we have
focused in this article on diamondoid structures and molecular computers
based on semiconductors such as diamond, it will probably be easier
to first make systems that rely on materials that are simpler to synthesize
but whose material properties are not as good as diamond. The general
concept of positional control, however, still applies. A future article
will discuss in greater detail the design of such simpler systems,
and how they can form a stepping stone to mature molecular manufacturing.

K.
Eric Drexler, “Molecular Nanomachines:
Physical Principles and Iimplementation Strategies,” Annu.
Rev. Biophys. Biomol. Struct. 23(June 1994):377-405;
http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.bb.23.060194.002113
(first page)ABSTRACT.
The goal of constructing artificial molecular machine systems able
to perform mechanosynthesis is beyond the immediate reach of current
laboratory techniques. Nonetheless, these systems can already be modeled
in substantial detail, and existing techniques enable steps toward
their implementation. Mechanosynthetic systems will rely on mechanical
positioning to guide and control the molecular interactions of chemical
synthesis. The effective concentration of a mechanically positioned
species depends on the temperature and on the stiffness of the positioning
system. These concentrations can be large (> 100 M) and localized
on a molecular scale. Background concentrations can approach zero,
thus enabling precise molecular control of the locations and sequences
of synthetic operations. Researchers have developed concepts for mechanosynthetic
systems and defined general technology requirements. One approach
to the fabrication of molecular machine systems is the development
of AFM-based mechanosynthetic devices. These would position molecules
by binding them to (for example) antibody fragments attached to an
AFM tip. Development of suitable monomers, binding sites, and reaction
sequences would then be a basis for the fabrication of complex mechanical
structures. Biological molecular machine systems rely on the self-assembly
of folded polymers. A review of progress in protein engineering suggests
that we have the means to design and synthesize protein-like molecules
with well-defined structures and excellent stability. Success in this
effort provides a basis for the design of self-assembling systems,
and experience with the design and supramolecular assembly of smaller
molecules is encouraging regarding the success of this next step.
Development of a molecular machine technology promises a wide range
of applications. Biological molecular machines synthesize proteins,
read DNA, and sense a wide range of molecular phenomena. Artificial
molecular machine systems could presumably be developed to perform
analogous tasks, but with more stable structures and different results
(e.g. reading DNA sequences into a conventional computer memory, rather
than transcribing them into RNA). Self-assembling structures are widely
regarded as a key to molecular electronic systems, which therefore
share an enabling technology with molecular machine systems. Finally,
studies suggest that the use of molecular machine systems to perform
mechanosynthesis of diverse structures (including additional molecular
machine systems) will enable the development and inexpensive production
of a broad range of new instruments and products. Laboratory research
directed toward this goal seems warranted.OVERVIEW. In this
review, I assess progress in the design and implementation of molecular
machine systems by focusing on the fundamental principles of mechanosynthesis
and emerging strategies for the synthesis and assembly of large (>106
atom) devices. This chapter describs existing knowledge and capabilities
from the perspective of molecular systems engineering and examines
key objectives in implementing molecular machine systems.

Ralph
C. Merkle, “Molecular
building blocks and development strategies for molecular nanotechnology,”
Nanotechnology 11(2000):89-99;http://www.zyvex.com/nanotech/mbb/mbb.htmlABSTRACT.
If we are to manufacture products with molecular precision, we must
develop molecular manufacturing methods. There are basically two ways
to assemble molecular parts: self assembly and positional assembly.
Self assembly is now a large field with an extensive body of research.
Positional assembly at the molecular scale is a much newer field which
has less demonstrated capability, but which also has the potential
to make a much wider range of products. There are many arrangements
of atoms which seem either difficult or impossible to make using the
methods of self assembly alone. By contrast, positional assembly at
the molecular scale should make possible the synthesis of a much wider
range of molecular structures. One of the fundamental requirements
for positional assembly of molecular machines is the availability
of molecular parts. One class of molecular parts might be characterized
as molecular building blocks, or MBBs. With an atom count ranging
anywhere from ten to ten thousand (and even more), such MBBs would
be synthesized and positioned using existing (or soon to be developed)
methods. Thus, in contrast to investigations of the longer term possibilities
of molecular manufacturing (which often rely on mechanisms and systems
that are likely to take many years or even decades to develop), investigations
of MBBs focus on nearer term developmental pathways.

Vasilii
I. Artyukhov, “A six degree
of freedom nanomanipulator design based on carbon nanotube bundles,”
Nanotechnology 21(2010):385304;http://iopscience.iop.org/0957-4484/21/38/385304/pdf/0957-4484_21_38_385304.pdfABSTRACT.
Scanning probe imaging and manipulation of matter presents is of crucial
importance for nanoscale science and technology. However, its resolution
and ability to manipulate matter at the atomic scale is limited by
the rather poor control over the fine structure of the probe. In the
present communication, a strategy is proposed to construct a molecular
nanomanipulator from ultrathin single-walled carbon nanotubes. Covalent
modification of a nanotube cap at predetermined atomic sites makes
the nanotube act as a support for a functional "tool-tip"
molecule. Then, a small bundle of nanotubes (3 or 4) with aligned
ends can act as an extremely high aspect ratio parallel nanomanipulator
for a suspended molecule, where protraction or retraction of individual
nanotubes results in a controlled tilting of the tool-tip in two dimensions.
Together with the usual SPM three degrees of freedom and augmented
with rotation of the system as a whole, the design offers six degrees
of freedom for imaging and manipulation of matter with precision and
freedom so much needed in modern nanotechnology. A similar design
might be possible to implement with other high-aspect ratio nanostructures,
such as oxide nanowires.NOTE: A possible
method for manipulating the DMS tooltips
described in Freitas
and Merkle (2008) is presented in this paper.

A.
Herman, “Tip-Based Nanofabrication
as a Rapid Prototyping Tool for Quantum Science and Technology,”
Reviews in Theor. Sci. 1(March 2013):3-33;
http://www.ingentaconnect.com/content/asp/rits/2013/00000001/00000001/art00002
(abstract)ABSTRACT.
Tip-Based Nanofabication as a Rapid Prototyping Tool for Quantum Science
and Technology discusses the development of cantilevered nanotips
techniques of quantum devices prototyping and how they evolved from
scanning probe microscopy. Also covered are the advantages and future
prospects of atomic resolution capability and how to use this enabling
technology as a rapid prototyping tool for quantum science and technology.

Molecular
Manipulation for Mechanosynthesis (Experimental)

D.M.
Eigler, E.K. Schweizer, “Positioning
Single Atoms with a Scanning Tunnelling Microscope,” Nature
344(5 April 1990):524-526;
http://www.nature.com/nature/journal/v344/n6266/abs/344524a0.html
(abstract)ABSTRACT.
Since its invention in the early 1980s by Binnig and Rohrer, the scanning
tunnelling microscope (STM) has provided images of surfaces and adsorbed
atoms and molecules with unprecedented resolution. The STM has also
been used to modify surfaces, for example by locally pinning molecules
to a surface and by transfer of an atom from the STM tip to the surface.
Here we report the use of the STM at low temperatures (4 K) to position
individual xenon atoms on a single-crystal nickel surface with atomic
precision. This capacity has allowed us to fabricate rudimentary structures
of our own design, atom by atom. The processes we describe are in
principle applicable to molecules also. In view of the device-like
characteristics reported for single atoms on surfaces, the possibilities
for perhaps the ultimate in device miniaturization are evident.NOTE:
This was the first experimental demonstration of mechanical atomic
manipulation using scanning tunneling microscopy. The design constraint
employed in this experiment (the use of chemically non-reactive atoms
on a metallic surface and cryogenic temperatures to exploit the weak
electrostatic interactions between xenon and nickel) is important
because it shows that even extremely weakly interacting components
can be assembled that persist over both assembly and characterization
procedures.

Wilson
Ho, Hyojune Lee, “Single
bond formation and characterization with a scanning tunneling microscope,”
Science 286(26 November 1999):1719-1722;http://www.physics.uci.edu/~wilsonho/stm-iets.htmlABSTRACT.
A scanning tunneling microscope (STM) was used to manipulate the bonding
of a carbon monoxide (CO) molecule and to analyze the structure and
vibrational properties of individual products. Individual iron (Fe)
atoms were evaporated and coadsorbed with CO molecules on a silver
(110) surface at 13 kelvin. A CO molecule was transferred from the
surface to the STM tip and bonded with an Fe atom to form Fe(CO).
A second CO molecule was similarly transferred and bonded with Fe(CO)
to form Fe(CO)2. Controlled bond formation and characterization
at the single-bond level probe chemistry at the spatial limit.NOTE: Ho and Lee's
work explicitly involves tunneling electrons, not mechanical forces,
in bond formation.

Saw-Wai
Hla, Ludwig Bartels, Gerhard Meyer, Karl-Heinz Rieder, “Inducing
All Steps of a Chemical Reaction with the Scanning Tunneling Microscope
Tip: Towards Single Molecule Engineering,” Phys.
Rev. Lett. 85(September 2000):2777-2780;
http://prola.aps.org/abstract/PRL/v85/i13/p2777_1
(abstract), http://www.phy.ohiou.edu/~hla/HLA2000-2.pdf
(paper)ABSTRACT.
All elementary steps of a chemical reaction have been successfully
induced on individual molecules with a scanning tunneling microscope
(STM) in a controlled step-by-step manner utilizing a variety of manipulation
techniques. The reaction steps involve the separation of iodine from
iodobenzene by using tunneling electrons, bringing together two resultant
phenyls mechanically by lateral manipulation and, finally, their chemical
association to form a biphenyl molecule mediated by excitation with
tunneling electrons. The procedures presented here constitute an important
step towards the assembly of individual molecules out of simple building
blocks in situ on the atomic scale.NOTE: This mechanosynthetic
experiment demonstrated the formation of biphenyl on a copper (111)
surface via the mechanical breaking of the iodobenzene carbon-iodine
bond with tunneling electrons and mechanical positioning of the benzene
radical into vicinity of a second benzene radical, all performed at
20 K. This first experiment demonstrated that chemical assembly is
possible on a surface using positional control of the reactants by
employing a weak chemical bond (carbon-iodine) that could be broken
readily while the starting molecule was still bound to the surface.
A reliance on large differences in chemical reactivity to aid in the
control of a multi-step assembly process is a common motif in synthetic
chemistry.

Saw-Wai
Hla, Karl-Heinz Rieder,“Engineering
of single molecules with a scanning tunneling microscope tip,”
Superlattices and Microstructures 31(2002):63-72;http://www.phy.ohiou.edu/~hla/20.pdfABSTRACT.
The rapid progress in molecular manipulation with a scanning tunneling
microscope (STM) tip opens up entirely new opportunities in nanoscience
and technology. With these advances, the ultimate chemical reaction
steps such as dissociation, diffusion, adsorption, readsorption, and
bond-formation processes become possible to be performed by using
the STM tip at the single molecule level with an atomic scale precision.
By using a variety of manipulation techniques in a systematic and
step by step manner, a complete chemical reaction sequence has been
induced with the STM tip leading to the synthesis of molecules on
an individual basis. In this paper, various STM manipulation techniques
useful in the single molecule engineering process are reviewed, and
their impact on the future of nanoscience and technology is discussed.

Saw-Wai
Hla, Karl-Heinz Rieder, “STM
control of chemical reactions: single-molecule synthesis,” Annu.
Rev. Phys. Chem. 54(2003):307-330; http://www.phy.ohiou.edu/~hla/HLA-annualreview.pdfABSTRACT.
The fascinating advances in single atom/molecule manipulation with
a scanning tunneling microscope (STM) tip allow scientists to fabricate
atomic-scale structures or to probe chemical and physical properties
of matters at an atomic level. Owing to these advances, it has become
possible for the basic chemical reaction steps, such as dissociation,
diffusion, adsorption, readsorption, and bond-formation processes,
to be performed by using the STM tip. Complete sequences of chemical
reactions are able to induce at a single-molecule level. New molecules
can be constructed from the basic molecular building blocks on a one-molecule-at-a-time
basis by using a variety of STM manipulation schemes in a systematic
step-by-step manner. These achievements open up entirely new opportunities
in nanochemistry and nanochemical technology. In this review, various
STM manipulation techniques useful in the single-molecule reaction
process are reviewed, and their impact on the future of nanoscience
and technology are discussed.

Anne-Sophie
Duwez, Stephane Cuenot, Christine Jérôme, Sabine Gabriel,
Robert Jérôme, Stefania Rapino, Francesco Zerbetto, “Mechanochemistry:
Targeted Delivery of Single Molecules,” Nature Nanotechnology
1(October 2006):122-125;
http://www.nature.com/nnano/journal/v1/n2/full/nnano.2006.92.htmlABSTRACT.
The use of scanning probe microscopy-based techniques to manipulate
single molecules and deliver them in a precisely controlled manner
to a specific target represents a significant nanotechnological challenge.
The ultimate physical limit in the design and fabrication of organic
surfaces can be reached using this approach. Here we show that the
atomic force microscope (AFM), which has been used extensively to
investigate the stretching of individual molecules, can deliver and
immobilize single molecules, one at a time, on a surface. Reactive
polymer molecules, attached at one end to an AFM tip, are brought
into contact with a modified silicon substrate to which they become
linked by a chemical reaction. When the AFM tip is pulled away from
the surface, the resulting mechanical force causes the weakest bond
— the one between the tip and polymer — to break. This
process transfers the polymer molecule to the substrate where it can
be modified by further chemical reactions.NOTE: This is
a demonstration of a mechanical placement and bond formation of a
simple organic polymer onto a modified silicon surface with retraction
of the AFM tip and breaking of the AMF/polymer interaction, thereby
leaving the molecule chemically bound to the surface at 295 K. This
first demonstration of nanoscale mechanochemistry combines positional
control of reactants with bond formation governed by proximity of
otherwise stable chemical moieties. This finding is significant to
near-term mechanosynthetic approaches to nanoscale assembly as it
demonstrates the combination of positional control of reactants with
understood reaction mechanisms to yield site-specific changes to a
chemical workspace (here, a functionalized silicon surface). Here
the mechanical positioning of a small, chemically-stable polymer and
formation of a surface-to-polymer amide bond generates a structure
strong enough to allow for retraction of the mechanical delivery system
(AFM tip), indicating that assembly processes can be designed and
performed using raw materials that may be otherwise chemically stable
systems. In effect, a building block need not be highly reactive,
but only contain a chemical functionality sensitive to the proximity
of other functional groups.

A.
Deshpande, H. Yildirim, A. Kara, D.P. Acharya, J. Vaughn, T.S. Rahman,
S.-W. Hla, “Atom-By-Atom
Extraction Using the Scanning Tunneling Microscope Tip-Cluster Interaction,”
Phys. Rev. Lett. 98(11 January 2007):028304;
http://www.phy.ohiou.edu/%7Ehla/HLA-46.pdf
(paper),
http://www.phy.ohiou.edu/%7Ehla/atom-extract/atom-extract.htm
(STM movie)ABSTRACT.
We investigate the atomistic details of a single atom-extraction process
realized by using the scanning tunneling microscope tip-cluster interaction
on a Ag(111) surface at 6 K. Single atoms are extracted from a silver
cluster one atom at a time using small tunneling biases less than
35 mV. Combined total energy calculations and molecular dynamics simulations
show a lowering of the atom-extraction barrier upon approaching the
tip to the cluster. Thus, a mere tuning of the proximity between the
tip and the cluster governs the extraction process. The atomic precision
and reproducibility of this procedure are demonstrated by repeatedly
extracting single atoms from a silver cluster on an atom-by-atom basis.NOTE: This three-dimensional
atomic disassembly of a small silver cluster on a silver (111) surface
at 6 K using a scanning tunneling microscope is significant as a demonstration
of the capability of three-dimensional control of disassembly at the
atomic scale. In effect, this study is the first to apply envisioned
top-down approaches for manufacturing complex structures via bulk
material disassembly at the atomic level, the same scale at which
envisioned bottom-up approaches may begin their fabrication processes.

S.K.
Kufer, E.M. Puchner, H. Gumpp, T. Liedl, H.E. Gaub, “Single-Molecule
Cut-and-Paste Surface Assembly,” Science
319(1 February 2008):594-596; http://www.sciencemag.org/cgi/content/full/319/5863/594
(paper) ABSTRACT.
We introduce a method for the bottom-up assembly of biomolecular structures
that combines the precision of the atomic force microscope (AFM) with
the selectivity of DNA hybridization. Functional units coupled to
DNA oligomers were picked up from a depot area by means of a complementary
DNA strand bound to an AFM tip. These units were transferred to and
deposited on a target area to create basic geometrical structures,
assembled from units with different functions. Each of these cut-and-paste
events was characterized by single-molecule force spectroscopy and
single-molecule fluorescence microscopy. Transport and deposition
of more than 5000 units were achieved, with less than 10% loss in
transfer efficiency.NOTE: This paper
is included in this bibliography as an example of positionally-controlled
mechanosynthesis using complementary biological molecules, with 5000
individual molecules installed one by one as array elements on a planar
grid to 10 nm positional accuracy using an AFM in aqueous medium.

Ying
Jiang, Qing Huan, Laura Fabris, Guillermo C. Bazan, Wilson Ho, “Submolecular
control, spectroscopy and imaging of bond-specific chemistry in single
functionalized molecules,” Nature Chemistry
5(2013):36-41; http://www.nature.com/nchem/journal/v5/n1/full/nchem.1488.html
(paper) ABSTRACT.
One of the key challenges in chemistry is to break and form bonds
selectively in complex organic molecules that possess a range of different
functional groups. To do this at the single-molecule level not only
provides an opportunity to create custom nanoscale devices, but offers
opportunities for the in-depth study of how the molecular electronic
structure changes in individual reactions. Here we use a scanning
tunnelling microscope (STM) to induce a sequence of targeted bond
dissociation and formation steps in single thiol-based p-conjugated
molecules adsorbed on a NiAl(110) surface. Furthermore, the electronic
resonances of the resulting species were measured by spatially resolved
electronic spectroscopy at each reaction step. Specifically, the STM
was used to cleave individual acetyl groups and to form Au–S
bonds by manipulating single Au atoms. A detailed understanding of
the Au–S bond and its non-local influence is fundamentally important
for determining the electron transport in thiol-based molecular junction.NOTE: "The
feasibility of initiating a bond-specific reaction within a complex
molecule with functional groups is more relevant to molecular nanotechnology,
in areas such as molecular electronics, organic solar cells and nanomachines."
Tunneling electrons are used to break bonds.

Hydrogen
Abstraction Tools (Theory)

Michael
Page, Donald W. Brenner,
“Hydrogen abstraction from a diamond surface: Ab initio
quantum chemical study using constrained isobutane as a model,”
J. Am. Chem. Soc. 113(1991):3270-3274; http://pubs.acs.org/cgi-bin/abstract.cgi/jacsat/1991/113/i09/f-pdf/f_ja00009a008.pdf
(first page)ABSTRACT.
Abstraction of terminal hydrogens on a diamond [111] surface by atomic
hydrogen has been offered as the possible rate-determining elementary
step in the mechanism of low-pressure diamond growth by chemical vapor
deposition. We use ab initio multiconfiguration self-consistent-field
methodsto
estimate the activation energy for this abstraction reaction. We do
this by first computing features of the potential energy surface for
hydrogen abstraction from gas-phase isobutane and then computing features
of the potential energy surface for this same system imposing constraints
that mimic those found in a diamond lattice. Our results indicate
that, although 5.4 kcal/mol of the CH bond energy in isobutane is
attributable to structural relaxation of the radical, most of this
radical relaxation energy (4.5 kcal/mol of it) is realized even with
geometric constraints similar to those in a diamond lattice. We therefore
predict bonds to a diamond surface to be only about 1 kcal/mol stronger
than corresponding bonds to a gas-phase tertiary-carbon atom. The
effect of the geometrical constraints on the activation energy for
the hydrogen abstraction reaction is even smaller: all but 0.2 kcal/mol
of the gas-phase radical relaxation energy at the transition state
is realized even with the imposition of lattice-type constraints.
Our results therefore support the use in kinetic modeling or molecular
dynamics simulations of activation energies taken from analogous gas-phase
hydrocarbon reactions with little or no adjustment.

Charles
B. Musgrave, Jason K. Perry, Ralph C. Merkle, William A. Goddard III,
“Theoretical studies of
a hydrogen abstraction tool for nanotechnology,” Nanotechnology
2(1991):187-195; http://www.zyvex.com/nanotech/Habs/Habs.htmlABSTRACT.
Processes that use mechanical positioning of reactive species to control
chemical reactions by either providing activation energy or selecting
between alternative pathways will allow us to construct a wide range
of complex molecular structures. An example of such a process is the
abstraction of hydrogen from diamond surfaces by a radical species
attached to a mechanical positioning device for synthesis of atomically
precise diamond-like structures. In the design of a nanoscale, site-specific
hydrogen abstraction tool, we suggest the use of an alkynyl radical
tip. Using ab initio quantum-chemistry techniques including
electron correlation we model the abstraction of hydrogen from dihydrogen,
methane, acetylene, benzene and isobutane by the acetylene radical.
Of these systems, isobutane serves as a good model of the diamond
(111) surface. By conservative estimates, the abstraction barrier
is small (less than 7.7 kcal mol-1) in all cases except
for acetylene and zero in the case of isobutane. Thermal vibrations
at room temperature should be sufficient to supply the small activation
energy. Several methods of creating the radical in a controlled vacuum
setting should be feasible. Thermal, mechanical, optical and chemical
energy sources could all be used either to activate a precursor, which
could be used once and thrown away, or alternatively to remove the
hydrogen from the tip, thus refreshing the abstraction tool for a
second use. We show how nanofabrication processes can be accurately
and inexpensively designed in a computational framework.

Xiao
Yan Chang, Martin Perry, James Peploski, Donald L. Thompson, Lionel
M. Raff,“Theoretical studies of
hydrogen-abstraction reactions from diamond and diamond-like surfaces,”
J. Chem. Phys. 99(15 September 1993):4748-4758;
http://link.aip.org/link/?JCPSA6/99/4748/1
(abstract)ABSTRACT.
Reaction probabilities, cross sections, rate coefficients, frequency
factors, and activation energies for hydrogen-atom abstraction from
a hydrogen-covered C(111) surface have been computed using quantum
wave packet and classical trajectory methods on the empirical hydrocarbon
#1 potential hypersurface developed by Brenner. Upper bounds for the
abstraction rates, activation energies, and frequency factors have
been obtained for six different chemisorbed moieties on a C(111) diamond
surface using a classical variational transition-state method. For
the hydrogen-covered surface, the results of the wave packet/trajectory
calculations give k(t) = 1.67 x 1014 exp(-0.46 eV/kbT)
cm3/mol s, which is about a factor of 2.9 less than the
gas-phase abstraction rate from tertiary carbon atoms at 1200 K. The
variational calculations show that the activation energies for hydrogen-atom
abstraction vary from 0.0 to 1.063 eV. Some sp2-bonded
hydrogen atoms can be removed in a barrierless process if adjacent
to a carbon radical. In contrast, abstractions that produce a methylene
carbon are associated with much larger activation energies in the
range 0.49-0.82 eV. Abstraction from nonradical chemisorbed ethylene
structures of the type that might be formed by the chemisorption of
acetylene at two lattice sites is a particularly slow process with
a 1.063 eV activation energy. Hydrogen abstraction from sp3
carbon atoms have activation energies ~0.4 eV. The results suggest
that phenomenological growth models which assume either an equilibrium
distribution between surface hydrogen/H2 or a common abstraction
rate for surface hydrogen atoms are unlikely to be accurate.

Susan
B. Sinnott, Richard J. Colton, Carter T. White, Donald W. Brenner,
“Surface patterning by
atomically-controlled chemical forces: molecular dynamics simulations,”
Surf. Sci. 316(1994):L1055-L1060; http://www.mse.ncsu.edu/CompMatSci/papers/N1_science.pdfABSTRACT.
The use of atomically-controlled reactive chemical forces via modified
scanning-probe microscope tips provides a potentially powerful way
of building nanodevices. In this work, we use atomistic simulations
to explore the feasibility of one such system, namely the selective
abstraction of hydrogen from a diamond surface using a tip with a
chemisorbed ethynyl radical.
We characterize reaction rates and energy flow at the tip, and conclude
that they are sufficiently fast to make this approach feasible. We
propose a novel tip design to perform the abstraction without inadvertently
damaging the surface or probe tip.

D.W.
Brenner, S.B. Sinnott, J.A. Harrison, O.A. Shenderova, “Simulated
engineering of nanostructures,” Nanotechnology
7(1996):161-167;http://www.zyvex.com/nanotech/nano4/brennerPaper.pdfABSTRACT.
Results are reported from two molecular-dynamics simulations designed
to yield insight into the engineering of nanometer-scale structures.
The first is the initial stages of the indentation of a silicon substrate
by an atomically-sharp diamond tip. Up to an indentation depth of
approximately 0.6 nm the substrate responds elastically and the profile
of the disturbed region of the substrate normal to the surface reflects
the shape of the tip apex. The disturbed region in the plane of the
surface, however, reflects the symmetry of the substrate rather than
that of the tip. As indentation progresses the damage to the substrate
becomes irreversible, and the profile of the damage normal to the
substrate surface approximately matches that of the tip, while the
in-plane profile appears roughly circular rather than displaying the
symmetry of either the tip or substrate. The tip maintains its integrity
throughout the simulation, which had a maximum indentation depth of
1.2 nm. The second study demonstrates patterning of a diamond substrate
using a group of ethynyl radicals attached to a diamond tip. The tip
is designed so that the terrace containing the radicals has an atomically-sharp
protrusion that can protect the radicals during a tip crash. At contact
between the tip and substrate the protrusion is elastically deformed,
and five of six chemisorbed radicals abstract hydrogen atoms during
the 1.25 picoseconds the tip is in contact with the surface. Displacement
of the tip an additional 2.5 Å, however, results in permanent
damage to the protrusion with little deformation of the substrate.

A.
Ricca, C.W. Bauschlicher Jr., J.K. Kang, C.B. Musgrave, “Hydrogen
abstraction from a diamond (111) surface in a uniform electric field,”
Surf. Sci. 429(1999):199-205.ABSTRACT.
Bond breaking in a strong electric field is shown to arise from a
crossing of the ionic and covalent asymptotes. The specific example
of hydrogen abstraction from a diamond (111) surface is studied using
a cluster model. The addition of nearby atoms in both the parallel
and perpendicular direction to the electric field are found to have
an effect. It is also shown that the barrier is not solely related
to the position of the ionic and covalent asymptotes.

Berhane
Temelso, C. David Sherrill, Ralph C. Merkle, Robert A. Freitas Jr.,
“High-level Ab Initio
Studies of Hydrogen Abstraction from Prototype Hydrocarbon Systems,”
J. Phys. Chem. A 110(28 September 2006):11160-11173;
http://pubs.acs.org/doi/abs/10.1021/jp061821e
(ACS abstract), http://www.MolecularAssembler.com/Papers/TemelsoHAbst.pdf
(paper).ABSTRACT.
Symmetric and non-symmetric hydrogen abstraction reactions are studied
using state-of-the-art ab initio electronic structure methods.
Second-order Moller-Plesset perturbation theory (MP2) and the coupled-cluster
singles, doubles and perturbative triples [CCSD(T)] methods with large
correlation consistent basis sets (cc-pVXZ, where X = D,T,Q) are used
in determining the transition-state geometries, activation barriers,
and thermodynamic properties of several representative hydrogen abstraction
reactions. The importance of basis set, electron correlation, and
choice of zeroth-order reference wavefunction in the accurate prediction
of activation barriers and reaction enthalpies are also investigated.
The ethynyl radical (•CCH), which has a very high affinity for
hydrogen atoms, is studied as a prototype hydrogen abstraction agent.
Our high-level quantum mechanical computations indicate that hydrogen
abstraction using the ethynyl radical is virtually barrierless for
hydrogens bonded to an sp3 carbon and has a barrier of
less than 3 kcal mol-1 for hydrogens bonded to an sp2
carbon. These low activation barriers further corroborate previous
studies suggesting that ethynyl-type radicals would make good tooltips
for abstracting hydrogens from diamondoid surfaces during mechanosynthesis.
Modeling the diamond C(111) surface with isobutane and treating the
ethynyl radical as a tooltip, hydrogen abstraction in this reaction
is predicted to be barrierless.

L.
Srinivasakannan, S. Kulandaivelu, M. Wuppalamarthi, “Terminal
alkynes as a position abstraction tool for the preparation of nano
materials ,” International Conference on Nanoscience and Nanotechnology
2008 (ICONN 2008), 25-29 February 2008, pp. 75-78; http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=4639249
(abstract)ABSTRACT.
The terminal alkyne residue, -CequivC . H is one of the most acidic
among the C-H groups (Pedireddy & Desiraju,1992). The ethynyl
or propargyl radical formed by removing the terminal hydrogen in an
alkyne is likely to have more affinity for hydrogen. It can be used
for removing the hydrogen atoms at desired places from diamondoid
structures in molecular manufacturing. Hence the terminal alkynes
can be used as position abstraction tool for hydrogen in the production
of nano materials (Musgrave et.al. 1991). The radical of a molecule
having the ethynyl or propargyl group at the end can be embedded into
structures that can act like the base of a handle. This arrangement
can act as an excellent tool tip. Hydrogen bonding plays an important
role in deciding the suitability of a terminal alkyne to act as a
tool tip molecule. An analysis of the crystallographic and spectrosc
opic data help us gain an insight into C-H...X hydrogen bond interactions
(Desiraju 1991, Steiner 2003). The single crystal X ray diffraction
studies reveal the three dimensional view of the molecule and provide
the inter molecular C ... O distances. Infrared (IR) spectroscopy
has a prominent place in the history of investigation of hydrogen
bonding (Mootz and Deeg 1992). The choice of terminal acetelenes to
act as a tool tip molecule can be made by taking into consideration
the evidence obtained from crystallographic and spectroscopic data.
The crystallographic (Lakshmi et al, 1996) and spectroscopic data
of 7beta hydroxy -7alpha-(3-propargyl)-3-methyl-spiro[5.5]undec- 2-en-l-one
are analysed.

Hydrogen
Abstraction Tools (Experimental)

J.W.
Lyding, K. Hess, G.C. Abeln, D.S. Thompson, J.S. Moore, M.C. Hersam,
E.T. Foley, J. Lee, Z. Chen, S.T. Hwang, H. Choi, P.H. Avouris, I.C.
Kizilyalli, “UHV-STM nanofabrication
and hydrogen/deuterium desorption from silicon surfaces: implications
for CMOS technology,” Appl. Surf. Sci.
130(June 1998):221-230.ABSTRACT:
The development of ultrahigh vacuum–scanning tunneling microscopy
(UHV–STM)-based nanofabrication capability for hydrogen passivated
silicon surfaces has opened new opportunities for selective chemical
processing, down to the atomic scale. The chemical contrast between
clean and H-passivated Si(100) surfaces has been used to achieve nanoscale
selective oxidation, nitridation, molecular functionalization, and
metallization by thermal chemical vapor deposition (CVD). Further
understanding of the hydrogen desorption mechanisms has been gained
by extending the studies to deuterated surfaces. In these experiments,
it was discovered that deuterium is nearly two orders of magnitude
more difficult to desorb than hydrogen in the electronic desorption
regime. This giant isotope effect provided the basis for an idea that
has since led to the extension of complementary metal oxide semiconductor
(CMOS) transistor lifetimes by factors of 10 or greater. Low temperature
hydrogen and deuterium desorption experiments were performed to gain
further insight into the underlying physical mechanisms. The desorption
shows no temperature dependence in the high energy electronic desorption
regime. However, in the low energy vibrational heating regime, hydrogen
is over two orders of magnitude easier to desorb at 11 K than at room
temperature. The enhanced desorption in the low temperature vibrational
regime has enabled the quantification of a dramatic increase in the
deuterium isotope effect at low voltages. These results may have direct
implications for low voltage and/or low temperature scaled CMOS operation.

E.T.
Foley, A.F. Kam, J.W. Lyding, P.H. Avouris, “Cryogenic
UHV-STM Study of Hydrogen and Deuterium Desorption from Si(100),”
Phys. Rev. Lett. 80(1998):1336-1339; http://prola.aps.org/abstract/PRL/v80/i6/p1336_1
(abstract)ABSTRACT:
A cryogenic UHV scanning tunneling microscope has been used to study
the electron stimulated desorption of hydrogen and deuterium from
Si(100) surfaces at 11 K. A strong isotope effect is observed, as
seen previously at room temperature. Above ~5 eV, the desorption yields
for H and D are temperature independent, while in the tunneling regime,
below 4 eV, H is a factor of ~300 easier to desorb at 11 than at 300
K. This large temperature dependence is explained by a model that
involves multiple vibrational excitation and takes into account the
increase of the Si-H(D) vibrational lifetime at low temperature.

L.J.
Lauhon, W. Ho, “Inducing
and Observing the Abstraction of a Single Hydrogen Atom in Bimolecular
Reactions with a Scanning Tunneling Microscope,” J.
Phys. Chem. 105(2000):3987-3992; http://pubs.acs.org/cgi-bin/abstract.cgi/jpcbfk/2001/105/i18/abs/jp002484r.html
(abstract)ABSTRACT:
A variable-temperature scanning tunneling microscope (STM) was used
to initiate and observe the abstraction of a single hydrogen atom
in a simple bimolecular reaction. Dicarbon (CC) on the Cu(001) surface
reacted separately with hydrogen sulfide (H2S)
and water (H2O) to form CCH + SH
and CCH + OH, respectively. At 9 K, hydrogen abstraction from H2O
occurred spontaneously upon contact between CC and thermally diffusing
H2O molecules. Hydrogen abstraction
from H2S was effected at 9 K by inducing
H2S diffusion via excitation with
tunneling electrons. The thermal diffusion and reaction of H2S
and CC were also observed at 45 K. By removing a single hydrogen atom
from H2S and H2O
using tunneling electrons, we established the identities of the sulfhydryl
(SH) and hydroxyl (OH) reaction products. SH and OH did not react
with CC under conditions that led to the reaction of the parent molecules.
The bimolecular reactions H2O + O
—> 2OH and H2S
+ O —>SH + OH did not occur thermally at 9 K but were induced
by tunneling electrons.

K.
Bobrov, A.J. Mayne, A. Hoffman, G. Dujardin, “Atomic-scale
desorption of hydrogen from hydrogenated diamond surfaces using the
STM,” Surface Science 528(20 March
2003):138-143; http://linkinghub.elsevier.com/retrieve/pii/S0039602802026237
(abstract)ABSTRACT:
Diamond has a number of unique chemical and physical properties. In
particular, when covered with hydrogen, diamond surfaces acquire a
negative electron affinity (NEA). This NEA property has already been
used to fabricate high-efficiency diamond-based light detectors and/or
electron emitters. We have used the scanning tunnelling microscope
for (i) atomic-scale visualisation of the hydrogenated diamond surface,
(ii) probing the surface electronic structure and (iii) atomic-scale
desorption of hydrogen atoms. Desorption of individual hydrogen atoms
has been used to pattern pre-selected areas on the hydrogenated diamond
surface. This is considered to be a promising way to fabricate atomic-scale
photon detectors and/or electron emitters. The
feasibility of the tip-induced atomic-scale desorption of hydrogen
from the diamond surface is discussed in comparison with the similar
studies on hydrogenated silicon and germanium surfaces performed previously.NOTE: This work
employed tunnel current flow, not mechanical forces, to break H bonds.

Satoshi
Katano, Yousoo Kim, Masafumi Hori, Michael Trenary, Maki Kawai, “Reversible
Control of Hydrogenation of a Single Molecule,” Science
316(29 June 2007):1883-1886; http://www.sciencemag.org/cgi/content/abstract/316/5833/1883
(abstract), http://www.sciencemag.org/cgi/content/full/316/5833/1883
(paper)ABSTRACT:
Low-temperature scanning tunneling microscopy was used to selectively
break the N-H bond of a methylaminocarbyne (CNHCH3) molecule
on a Pt(111) surface at 4.7 kelvin, leaving the C-H bonds intact,
to form an adsorbed methylisocyanide molecule (CNCH3).
The methylisocyanide product was identified through comparison of
its vibrational spectrum with that of directly adsorbed methylisocyanide
as measured with inelastic electron tunneling spectroscopy. The CNHCH3
could be regenerated in situ by exposure to hydrogen at room temperature.
The combination of tip-induced dehydrogenation with thermodynamically
driven hydrogenation allows a completely reversible chemical cycle
to be established at the single-molecule level in this system. By
tailoring the pulse conditions, irreversible dissociation entailing
cleavage of both the C-H and N-H bonds can also be demonstrated.NOTE:
As with earlier work, this effort employed tunnel current flow, not
purely mechanical forces, to break the H bond.

Hydrogen
Donation Tools (Theory)

Berhane
Temelso, C. David Sherrill, Ralph C. Merkle, Robert A. Freitas Jr.,
“Ab
Initio Thermochemistry of the Hydrogenation
of Hydrocarbon Radicals Using Silicon, Germanium, Tin and Lead Substituted
Methane and Isobutane,”
J. Phys. Chem. A 111(15 August 2007):8677-8688.http://pubs.acs.org/doi/abs/10.1021/jp071797k (ACS abstract), http://www.MolecularAssembler.com/Papers/TemelsoHDon.pdf
(paper).ABSTRACT.
A series of reactions of the type Y• + XH4 —>
YH + •XH3
and Y'•
+ HX(CH3)3—>
Y'H + •X(CH3)3
where Y=H, CH3; Y'=CH3, C(CH3)3;
and X=Si, Ge, Sn, Pb are studied using state-of-the-art ab initio
electronic structure methods. Second-order Möller-Plesset perturbation
theory (MP2), the coupled-cluster singles, doubles and perturbative
triples [CCSD(T)] method, and density functional theory (DFT) are
used with correlation-consistent basis sets (cc-pVNZ, where N = D,
T, Q) and their pseudopotential analogs (cc-pVNZ-PP) in order to determine
the transition-state geometries, activation barriers, and thermodynamic
properties of these reactions. Trends in the barrier heights as a
function of the group IVA atom (Si, Ge, Sn, and Pb) are examined.
With respect to kinetics and thermodynamics, the use of a hydrogen
attached to a group IVA element as a possible hydrogen donation tool
in the mechanosynthesis of diamondoids appears feasible.

Hydrogen
Donation Tools (Experimental)

B.J.
McIntyre, M. Salmeron, G.A. Somorjai, “Nanocatalysis
by the tip of a scanning tunneling microscope operating inside a reactor
cell,” Science 265(2 September 1994):1415-1418.ABSTRACT.
The platinum-rhodium tip of a scanning tunneling microscope that operates
inside of an atmospheric-pressure chemical reactor cell has been used
to locally rehydrogenate carbonaceous fragments deposited on the (111)
surface of platinum. The carbon fragments were produced by partial
dehydrogenation of propylene. The reactant gas environment inside
the cell consisted of pure H2 or a 1:9 mixture of CH3CHCH2
and H2 at 300 kelvin. The platinum-rhodium tip acted as
a catalyst after activation by short voltage pulses. In this active
state, the clusters in the area scanned by the tip were reacted away
with very high spatial resolution.

Wolfgang
T. Muller, David L. Klein, Thomas Lee, John Clarke, Paul L. McEuen,
Peter G. Schultz, “A strategy
for the chemical synthesis of nanostructures,” Science
268(14 April 1995):272-273.ABSTRACT.
Highly localized chemical catalysis was carried out on the surface
groups of a self-assembled monolayer with a scanning probe device.
With the use of a platinum-coated atomic force microscope tip, the
terminal azide groups of the monolayer were catalytically hydrogenated
with high spatial resolution. The newly created amino groups were
then covalently modified to generate new surface structures. By varying
the nature of the catalyst and the chemical composition of the surface,
it may be possible to synthesize molecular assemblies not readily
produced by existing microfabrication techniques.

D.H.
Huang, Y. Yamamoto, “Physical
mechanism of hydrogen deposition from a scanning tunneling microscopy
tip,” Appl. Phys. A 64(April 1997):R419-R422.ABSTRACT.
We report on the first successful deposition of individual hydrogen
atoms from a tungsten tip of a scanning tunneling microscope onto
a monohydride Si(100)-221:H surface. Hydrogen atoms adsorbed on the
tungsten tip are first diffused to the tip apex from the surroundings
of the tip by the application of +3.5 V bias to the sample for ~300
ms, and subsequently deposited onto the surface by the application
of -8.5 V 300 ms pulses to the sample. The physical mechanisms involved
are hydrogen diffusion on the tip via field-gradient-induced diffusion
and hydrogen deposition due to electronic excitation.

C.
Thirstrup, M. Sakurai, T. Nakayama, M. Aono, “Atomic
scale modifications of hydrogen-terminated silicon 2 x 1 and 3 x 1
(001) surfaces by scanning tunneling microscope,” Surf.
Sci. 411(1998):203-214.ABSTRACT.
Atomic scale desorption and deposition of hydrogen (H) atoms on Si(001)-(2
x 1)-H and Si(001)-(3 x 1)-H surfaces have been studied using clean
and H covered tips from a scanning tunneling microscope. We report
desorption of H atoms from these surfaces at positive and negative
sample bias voltages with a resolution of one to two atomic rows and
atomic scale phase transitions from 3 x 1 structures to 2 x 1 structures
and vice versa. At positive sample bias, phase transitions from the
3 x 1 to 2 x 1 structures are accompanied with a large number of dangling
bonds on the newly crated 2 x 1 structures, because the desorption
of H from the 2 x 1 structure occurs at a lower tunnel current than
the formation of the phase transition. At negative sample bias -5
V, the situation is reversed with the desorption from the 2 x 1 structure
occurring at a larger tunnel current than the formation of the phase
transition, and “clean” local 2 x 1 structures with few
dangling bonds can be achieved. Using H covered tips and increasing
the substrate temperatures of Si(001)-(2 x 1)-H surfaces to approximate
to 400 K, opposite local phase transitions from 2 x 1 structure to
3 x 1 structures are also reported, but such phase transitions were
only observed at negative sample bias.

Diamond
Mechanosynthesis Tools (Theory)

Stephen
P. Walch, Ralph C. Merkle, “Theoretical
studies of diamond mechanosynthesis reactions,” Nanotechnology
9(December 1998):285-296;http://www.zyvex.com/nanotech/mechanosynthesis.htmlABSTRACT.
Density functional theory methods have been used to examine the interaction
of i) the carbene and C2 tools with a pair of radical sites
on the diamond (111) surface and ii) the carbene tool with a surface
dimer on the reconstructed diamond (100) surface. For the (111) surface,
the carbene tool (carbenecyclopropene) is found to bond preferentially
to a single radical site (on top site) rather than at a bridged site.
This means this tool is not useful for adding a carbon to diamond
(111). The C2 tool, on the other hand, is found to add
a bridged C2 molecule, through a series of steps which
are overall exothermic. The carbene tool can add a carbon to the bridged
C2 molecule, leading to a bridged C3 molecule
perpendicular to the surface, by an overall exothermic series of steps.
If another radical site is activated, the C3 can bend over
to a three fold coordinated position, with only a small barrier. Thus,
this series of steps can be used to create a three fold coordinated
C3 molecule on the diamond (111) surface. For the surface
dimer on the reconstructed (100) surface, the carbene tool is found
to add with no barrier if the angle between the tool and the surface
is allowed to vary or with a 0.09 aJ (13 kcal/mol) barrier for a C2v
constrained approach. In this case, a bridged site is strongly favored,
and the subsequent steps of sequentially breaking the p and s bonds
between the tool and added carbon atom are all feasible. Thus, this
series of steps can add a bridged C atom to the reconstructed diamond
(100) surface.

Fedor
N. Dzegilenko, Deepak Srivastava, Subhash Saini, “Simulations
of carbon nanotube tip assisted mechano-chemical reactions on a diamond
surface,” Nanotechnology 9(December
1998):325-330;http://web.archive.org/web/20000605131223/http://www.nas.nasa.gov/~fedor/node_final.htmlABSTRACT.
The interaction of a carbon nanotube tip with two chemically modified
caps with a single-height-stepped C100-(2x1) diamond surface is studied
by performing molecular dynamics simulations. The C2 and
C6H2 radicals are attached to the end cap of
nanotube. The forces for solving the classical equations of motion
are derived from Brenner's many-body reactive potential. Depending
on the surface impact site, the nanotube initial velocity towards
the diamond surface, and the nanotube withdrawal rate a variety of
mechanochemical reactions have been observed. The strong tip-surface
interaction results in creation of chemically different nanostructures
on the diamond surface for C6H2 tip, while the
tip with C2 allows to remove a dimer of carbon atoms from
the upper-terrace of diamond. The possibility of using nanotube with
chemically modified caps for selective etching and nano-lithography
on different semiconductor surfaces is discussed.

Ralph
C. Merkle, Robert A. Freitas Jr., “Theoretical
analysis of a carbon-carbon dimer placement tool for diamond mechanosynthesis,”
J. Nanosci. Nanotechnol. 3(August 2003):319-324;http://www.MolecularAssembler.com/Papers/JNNDimerTool.pdf
or http://www.rfreitas.com/Nano/JNNDimerTool.pdf
or http://www.rfreitas.com/Nano/DimerTool.htmABSTRACT.
Density functional theory is used with Gaussian 98 to analyze a new
family of proposed mechanosynthetic tools that could be employed for
the placement of two carbon atoms—a carbon-carbon (CC) dimer—on
a growing diamond surface at a specific site. The analysis focuses
on specific group IV-substituted biadamantane tooltip structures and
evaluates their stability and the strength of the bond they make with
the CC dimer. These tools should be stable in a vacuum and should
be able to hold and position a CC dimer in a manner suitable for positionally
controlled diamond mechanosynthesis at room temperature.NOTE:
The DCB6 tooltip motif detailed here, initially disclosed at a Foresight
Conference in 2002, was the first complete tooltip ever proposed
(and computationally studied using ab initio techniques)
for the positionally-controlled deposition of carbon atoms (as dimers)
on a diamond surface.

Jingping
Peng, Robert A. Freitas Jr., Ralph C. Merkle, “Theoretical
analysis of diamond mechanosynthesis. Part I. Stability of C2
mediated growth of nanocrystalline diamond C(110) surface,”
J. Comput. Theor. Nanosci. 1(March 2004):62-70;http://www.MolecularAssembler.com/Papers/JCTNPengMar04.pdfABSTRACT.
A theoretical investigation of the chemical vapor deposition (CVD)
growth on clean diamond C(110) surfaces from carbon dimer precursors
shows that isolated deposited C2 dimers appear stable at
room temperature, but a second carbon dimer subsequently chemisorbed
in close vicinity to the first can adopt one of 19 local energy minima,
five of which require barriers >0.5 eV to reach the global minimum
and thus constitute stabilized defects. Three chemisorbed C2
dimers can adopt one of 35 local minimum energy structures, ten of
which are stable defects located in deep potential energy wells. The
number of potential defects increases with the number of deposited
carbon dimers which suggests an isolated rather than clustered growth
mechanism in CVD on bare diamond C(110). These results also provide
information regarding outcomes of the misplacement of a carbon dimer
and establish constraints on the required dimer-placement positional
precision that would be needed to avoid the formation of stable defects
during diamond surface growth.

David
J. Mann, Jingping Peng, Robert A. Freitas Jr., Ralph C. Merkle, “Theoretical
analysis of diamond mechanosynthesis. Part II. C2 mediated
growth of diamond C(110) surface via Si/Ge-triadamantane dimer placement
tools,” J. Comput. Theor. Nanosci.
1(March 2004):71-80; http://www.MolecularAssembler.com/Papers/JCTNMannMar04.pdfABSTRACT.
This paper presents a computational and theoretical investigation
of the vacuum mechanosynthesis of diamond on the clean C(110) surface
from carbon dimer (C2) precursors positionally constrained
throughout the reaction pathway by silicon- or germanium-doped triadamantane
derivatives mounted on a scanning probe tip. Interactions between
the dimer placement tools and the bare diamond C(110) surface are
investigated using Density Functional Theory (DFT) with generalized
gradient approximation (GGA) by constructing the reaction path potential
energy profiles and analyzing ab initio molecular dynamics
simulations. Similar methods are applied to study the energetics and
kinetics of recharging the tool with acetylene. Molecular mechanics
simulations on extended tool tips are carried out to elucidate the
positional uncertainty of the carbon dimer due to thermal fluctuations,
and the possibility of intermolecular dimerization and dehydrogenation
of the dimer placement tools is explored.

Damian
G. Allis, K. Eric Drexler, “Design
and Analysis of a Molecular Tool for Carbon Transfer in Mechanosynthesis,”
J. Comput. Theor. Nanosci. 2(March 2005):45-55;http://e-drexler.com/d/05/00/DC10C-mechanosynthesis.pdfABSTRACT.
Mechanosynthesis of a target class of graphene-, nanotube-, and diamond-like
structures will require molecular tools capable of transferring carbon
moieties to structures that have binding energies per atom in the
range of 1.105 to 1.181 aJ (159 to 170 kcal/mole). Desirable properties
for tools include exoergic transfer of moieties to these structures,
good geometrical exposure of moieties, and structural, electronic,
and positional stability. We introduce a novel carbon-transfer tool
design (DC10c), the first predicted to exhibit these properties in
combination. The DC10c tool is a stiff hydrocarbon structure that
binds carbon dimers through strained s-bonds. On dimer removal, diradical
generation at the dimer-binding sites is avoided by means of p-delocalization
across the binding face of the empty form, creating a strained aromatic
ring. Transfer of carbon dimers to each of the structures in the target
class is exoergic by a mean energy > 0.261 aJ per dimer (> 38
kcal/mole); this is compatible with transfer-failure rates ~ 10-24
per operation at 300 K. We present a B3LYP/6-31G(d,p) study of the
geometry and energetics of DC10c, together with discussion of its
anticipated reliability in mechanosynthetic applications.

Jingping
Peng, Robert A. Freitas Jr., Ralph C. Merkle, James R. Von Ehr, John
N. Randall, George D. Skidmore, “Theoretical
Analysis of Diamond Mechanosynthesis. Part III. Positional C2
Deposition on Diamond C(110) Surface using Si/Ge/Sn-based Dimer Placement
Tools,” J. Comput. Theor. Nanosci.
3(February 2006):28-41; http://www.MolecularAssembler.com/Papers/JCTNPengFeb06.pdfABSTRACT.
This paper extends an ongoing computational and theoretical investigation
of the vacuum mechanosynthesis of diamond on a clean C(110) diamond
surface from carbon dimer (C2) precursors, using Si-, Ge-
and Sn-substituted triadamantane-based positionally-controlled DCB6
dimer placement tools. Interactions between the dimer placement tools
and the C(110) surface are investigated by means of stepwise ab
initio molecular dynamics (AIMD) simulations, using Density Functional
Theory (DFT) with generalized gradient approximation (GGA), implemented
in the VASP software package. The Ge-based tool tip provides better
functionality over a wider range of temperatures and circumstances
(as compared with the Si or Sn tool tips ). The transfer of a single
carbon dimer from the Si-based tool tip onto C(110) is not controllable
at 300 K but is workable at 80 K; the Ge-based tool remains workable
up to 300 K. Geometry optimization suggests the Sn-based tool deposits
reliably but the discharged tool is distorted after use; stepwise
AIMD retraction simulations (at 300 K for the Sn tip) showed tip distortion
with terminating Sn atoms prone to being attracted towards the surface
carbon atoms. Stepwise AIMD shows successful placement of a second
dimer in a 1-dimer gapped position, and successful intercalation of
a third dimer into the 1-dimer gap between two previously deposited
dimers, on clean C(110) at 300 K using the Ge tool. Maximum tolerable
dimer misplacement error, investigated by stepwise AIMD quantification,
is 0.5 Å in x (across trough) and 1.0 Å in y (along trough)
for a positionally-correct isolated C2 deposition, and
1.0 Å in x and 0.3 Å in y for C2 intercalation
between two gapped ad-dimers. Rotational misplacement tolerances for
dimer placement are ±30° for the isolated dimer and -10&deg/+22.5&deg
for the intercalated dimer in the xy plane, with a maximum tolerable
“in plane” tip rolling angle of 32.5&deg and “out-of-plane”
tip rocking angle of 15&deg for isolated dimer. Classical molecular
dynamics (MD) analysis of a new Ge tooltip + handle system at 80 K
and 300 K found that dimer positional uncertainty is halved by adding
a crossbar in the most compliant direction. We conclude that the Si-based
and Ge-based tools can operate successfully at appropriate temperatures,
including up to room temperature for the Ge-based tool.NOTE: This paper
reports that the most-studied mechanosynthesis tooltip motif (DCB6Ge)
successfully places a C2 carbon dimer on a C(110) diamond
surface at both 300K (room temperature) and 80K (liquid nitrogen temperature),
and that the silicon variant (DCB6Si) also works at 80K but not at
300K. Maximum acceptable limits for tooltip translational and rotational
misplacement errors are reported in the paper. Over 100,000 CPU hours
were invested in this study. The DCB6 tooltip motif remains (in 2006)
the only tooltip motif that has been successfully simulated for its
intended function on a full (200-atom) diamond surface.

Robert
A. Freitas Jr., “A
Simple Tool for Positional Diamond Mechanosynthesis, and its Method
of Manufacture,” U.S. Patent No. 7,687,146,
issued 30 March 2010; http://www.MolecularAssembler.com/Papers/US7687146.pdfABSTRACT.
A method is described for building a mechanosynthesis tool intended
to be used for the molecularly precise fabrication of physical structures
-- as for example, diamond structures. An exemplar tool consists of
a bulk-synthesized dimer-capped triadamantane tooltip molecule which
is initially attached to a deposition surface in tip-down orientation,
whereupon CVD or equivalent bulk diamond deposition processes are
used to grow a large crystalline handle structure around the tooltip
molecule. The large handle with its attached tooltip can then be mechanically
separated from the deposition surface, yielding an integral finished
tool that can subsequently be used to perform diamond mechanosynthesis
in vacuo. The present disclosure is the first description of a complete
tool for positional diamond mechanosynthesis, along with its method
of manufacture. The same toolbuilding process may be extended to other
classes of tooltip molecules, other handle materials, and to mechanosynthetic
processes and structures other than those involving diamond.NOTE: This is
the first U.S. patent ever issued for positional mechanosynthesis.

Damian
G. Allis, Brian Helfrich, Robert A. Freitas Jr., Ralph C. Merkle,
“Analysis of Diamondoid
Mechanosynthesis Tooltip Pathologies Generated via a Distributed Computing
Approach,” J. Comput. Theor. Nanosci.
8(July 2011):1139-1161; http://www.ingentaconnect.com/content/asp/jctn/2011/00000008/00000007/art00009
(abstract), http://www.molecularassembler.com/Papers/AllisHelfrichFreitasMerkle2011.pdf
(paper)ABSTRACT.
The results of a combined molecular dynamics/quantum chemistry pathology
study of previously reported organic (diamondoid) tooltips for diamondoid
mechanosynthesis (DMS) are presented. This study, employing the NanoHive@Home
(NH@H) distributed computing project, produced 80,000 tooltip geometries
used in 200,000 calculations optimized at either the RHF/3-21G or
RHF/STO-3G levels of theory based on geometries obtained from high-energy
molecular dynamics simulations to produce highly deformed starting
geometries. These 200,000 calculations have been catalogued, grouped
according to energies and geometries, and analyzed to consider potentially
accessible defect structures (pathologies) for tooltip geometries
either binding a carbon dimer (C2)
feedstock or not containing the transported dimer feedstock. The transport
and deposition of feedstock and the stability of the tooltip between
dimer “loading” cycles are important geometries that must
be considered as part of a tooltip stability analysis. The NH@H framework
is found to be a useful method both for the study of highly deforming
covalent geometries and, using lower-temperature MD simulations, for
generating and optimizing molecular conformations (demonstrated using
biotin, n-heptane, and n-octane in this study).
The results of the pathology survey are discussed and general considerations
for the exploration of DMS tooltip usability are explored.

A.
Herman, “Toward Mechanosynthesis
of Diamondoid Structures: X. Commercial Capped CNT SPM Tip as Nowadays
Available C2 Dimer Placement Tool for Tip-Based Nanofabrication
,” J. Comput. Theor. Nanosci. 10(September
2013):2113-2122; http://www.ingentaconnect.com/content/asp/jctn/2013/00000010/00000009/art00031
(abstract)ABSTRACT.
According to Drexler, advanced mechanosynthesis will employ advanced
nano-machines, but advanced nano-machines will themselves be products
of advanced mechanosynthesis. This circular relationship must be broken
via TBN technology development. In this article, the possibility of
using easily available commercial CNT tips to assemble carbon-based
intermediate generations of nano-devices is considered. Mechanosynthesis
of a target class of carbon-based nano-devices will require molecular
tools capable of transferring C2 molecules to reaction
sites that have binding energies in the range of -6.9 to -7.4 eV per
carbon atom or -7.6 to -8.6 eV per C2 molecule. Desirable
properties of tools include approximately exoergic transfer of moieties
to these structures; good geometrical exposure of moieties; and structural,
electronic and positional stability. The results presented in this
paper suggest that the CNT tips now available on the market have adequate
properties to become tools for C2 molecule transfer into
a reaction site during positional mechanosynthesis. The surpassing
features of the commercial single/double wall capped CNT tips such
as, small tip radii, extreme aspect ratio, excellent wear-out behavior
and the average low temperature binding energy of C2 ~-5.0±1.2
eV make them the ideal tools for bridging the gap between present-day
tip-based nanofabrication (TBN) and future implementation of advanced
nanotechnology.

Diamond
Mechanosynthesis Tools (Experimental)

No entries.

Silicon/Germanium
Mechanosynthesis Tools (Theory)

A.
Herman, “Towards mechanosynthesis
of diamondoid structures. I. Quantum-chemical molecular dynamics simulations
of silaadamantane synthesis on hydrogenated Si(111) surface with the
STM,” Nanotechnology 8(September 1997):132-144.ABSTRACT.
The controlled manipulation of silicon atoms and silylene molecules
at the subnanometer scale via the scanning tunneling microscope (STM)
tip provides a potentially powerful way of building silicon diamondoid
structures. In this paper, we use quantum-chemical atomistic simulations
to explore the feasibility of silaadamantane mechanosynthesis on a
hydrogenated Si(111) surface using the STM tip. A sequence of energetically
favorable insertion reactions is established leading to stable surface
intermediates and finally to the simplest silicon diamondoid structure.
The sequence is based solely on these three reactants with the overall
charge neutrality of the structure maintained. We characterize reaction
rates and energy flows, and conclude that they are sufficiently fast
and simple to make this mechanosynthesis feasible.

A.
Herman, “Towards mechanosynthesis
of diamondoid structures. II. Quantum-chemical molecular dynamics
simulations of mechanosynthesis on an hydrogenated Si(111) surface
with STM,” Modeling Simul. Mater. Sci. Eng.
7(January 1999):43-58; http://www.iop.org/EJ/abstract/0965-0393/7/1/004
(abstract)ABSTRACT.
The controlled manipulation of silicon atoms and silylene molecules
at the subnanometre scale via a scanning tunnelling microscope (STM)
W tip provides a potentially powerful way of building silicon diamondoid
structures. In this work, we use quantum-chemical atomistic simulations
to explore the feasibility of mechanosynthesis on an hydrogenated
Si(111) surface using a STM tip. A sequence of energetically favourable
insertion reactions is established leading to stable surface intermediates.
This sequence of operations is sufficient to build an indefinitely
large volume of diamondoid lattice. The sequence is based solely on
two reactants (Si and SiH2) with
the overall charge neutrality of the structure maintained. We characterize
reaction rates and energy flows and conclude that they are sufficiently
fast and simple to make this mechanosynthesis feasible.

A.
Herman, “Toward Mechanosynthesis
of Diamondoid Structures: V. Silicon as the Material of Choice for
Preliminary Implementation of Intermediate Generation of Nano-Machine
Systems,” J. Comput. Theor. Nanosci.
7(August 2010):1482-1485; http://www.ingentaconnect.com/content/asp/jctn/2010/00000007/00000008/art00022
(abstract)ABSTRACT.
Using recently introduced by Drexler "lattice-scaled modulus"
Klm, two potential nano-materials were compared, i.e., silicon and
diamond. Detailed comparisons of physical and chemical properties
have shown that silicon can be considered as the material of choice
for a preliminary implementation of intermediate generation of nano-systems.

A.
Herman, “Toward Mechanosynthesis
of Diamondoid Structures: VI. Quantum-Chemical Molecular Dynamics
Comparison of Conditions for the STM Tip Driven Mechanosynthesis on
Hydrogenated Si(111), Si(110) and Si(100) Surfaces,” J.
Comput. Theor. Nanosci. 7(November 2010):2360-2366;
http://www.ingentaconnect.com/content/asp/jctn/2010/00000007/00000011/art00015
(abstract)ABSTRACT.
A possibility to prototype the silicon-based intermediate generations
of nano-devices using the STM caped SWCNT tip driven mechanosynthesis
on hydrogen passivated Si(111), Si(110) and Si(100) surfaces was studied
by means of the quantum-chemical molecular dynamics method. The proposed
strategy is an additive positional molecular manufacturing process
which uses a silicon atom (Si) and silylene molecule (SiH2 transfers
from caped SWCNT tip to the reaction center on hydrogenated silicon
surface to build parts of the silicon layer one at a time. Layers
can be generated automatically from 3D CAD models used on the UHV
STM machine, although nowadays they may also be manipulated manually.
A recently published (J. Comput. Theor. Nanosci…) detailed comparison
of physical and chemical properties of silicon and diamond has demonstrated
that silicon can be considered as the material of choice for a preliminary
implementation of intermediate generation of nano-systems. The work
presented here suggests that the proposed prototyping technology can
be used to manufacture production-quality parts of nano-systems in
relatively small numbers.

A.
Herman, “Toward Mechanosynthesis
of Diamondoid Structures: VII. Simple Strategy of Building Atomically
Perfect SPM Tip Through Attachment of C60 Molecule to Commercial Silicon
Tip by Controlled Hydrogen Atom Desorption from Tip Asperity Si(111)
Silicon Surface,” J. Comput. Theor. Nanosci.
8(September 2011):1703-1709; http://www.ingentaconnect.com/content/asp/jctn/2011/00000008/00000009/art00010
(abstract)ABSTRACT.
Tip manufacturers offer micro-fabricated silicon tips in three geometries,
i.e., pyramidal, tetrahedral and conical. Conical tips can be made
sharp, with high aspect ratios and radii as small as 50 Å. Pyramidal
tips have lower aspect ratios and nominal tip radii of a few hundred
angstroms, but they are more durable. However, even commercial conical
tip manufacturers supply the tip structure only at the micrometer
scale, and there is no direct method for imaging the very end of the
tip, i.e., the “nano-tip.“ In this paper a very simple
strategy of building atomically defined asperity on Si(111) surface
of the commercial silicon tip is described. The strategy consists
of four simple steps. In the first step, the silicon tip is irradiated
with ultraviolet light in the atmosphere of oxygen to remove carbon
contaminants. During the second step, a thermally oxidized SiO2 layer
is eliminated by HF etching to sharpen the tip apex and hydrogenation
of its surface. In the third step, controlled electron-stimulated
desorption of hydrogen from the tip asperity surface is applied. Finally,
in the step four, the C60 molecule docking to surface dangling bonds
is performed. In the final part of this work PM6 modeling was used
to show positional mechano-synthetic capabilities of the described
SPM tip.

A.
Herman, “Toward Mechanosynthesis
of Diamondoid Structures: VIII. Quantum-Chemical Molecular Dynamics
Simulations of Hexagonal Silicon-IV Structure Synthesis with STM,”
J. Comput. Theor. Nanosci. 8(October 2011):1982-1985;
http://www.ingentaconnect.com/content/asp/jctn/2011/00000008/00000010/art00014
(abstract)ABSTRACT.
As originally pointed out by Drexler, members of the broad class of
diamondoids can differ from diamond both in respect to bonding pattern
and elemental composition. In this paper the strategy of positional
mechanosynthesis of hexagonal silicon-IV structures is studied by
quantum-chemical molecular dynamics simulations. The estimated mechanosynthesis
conditions together with the general knowledge of silicon chemistry
suggest that the hexagonal polytype Si-IV, also termed as lonsdaleite
Si, is probably readily accessible by UHV-SPM tip driven mechanosynthesis.

A.
Herman, “Toward Mechanosynthesis
of Diamondoid Structures: IX. Commercial Capped CNT Scanning Probe
Microscopy Tip as Nowadays Available Tool for Silylene Molecule and
Silicon Atom Transfer,” J. Comput. Theor. Nanosci.
9(December 2012):2240-2244; http://www.ingentaconnect.com/content/asp/jctn/2012/00000009/00000012/art00038
(abstract)ABSTRACT.
According to Drexler, advanced mechanosynthesis will employ advanced
nanomachines, but advanced nanomachines will themselves be a product
of advanced mechanosynthesis. This circular relationship must be resolved
via SPM technology development. In this article the possibility of
using easily available commercial CNT tips to assembly silicon-based
intermediate generations of nanodevices is considered. Mechanosynthesis
of a target class of silicon-based nano-devices will require molecular
tools capable of transferring SiH2 molecules and Si atoms
to reaction centers that have binding energies within -2.9 ±
0.2 eV and -6.8 ± 0.3 eV, respectively. Desirable properties
for tools include near exoergic transfer of moieties to these structures;
good geometrical exposure of moieties; and structural, electronic,
and positional stability. The results presented in this paper suggest
that CNT tips presently available on the market have properties enabling
them to become tools for silylene molecule and silicon atom transfer
into a reaction center during positional mechanosynthesis. The surpassing
features of the commercial single/double wall capped CNT tips, such
as small tip radii, extreme aspect ratio, excellent wear-out behavior
and the average binding energy of ~ -3.2 eV (for SiH2 and
~ -6.0 eV (for Si), make them ideal tools for bridging present day
SPM technology and the future implementation of intermediate silicon-based
nanotechnology.

Silicon/Germanium
Mechanosynthesis Tools (Experimental)

R.S.
Becker, J.A. Golovchenko, B.S. Swartzentruber, “Atomic-scale
surface modifications using a tunneling microscope,” Nature
325(29 January 1987):419-421; http://www.nature.com/nature/journal/v325/n6103/abs/325419a0.html
(abstract), http://jw.nju.edu.cn/jingpin/courseware/daxuewulixue/register/creferences/ref/24_5.pdf
(paper)ABSTRACT:The desire to modify materials on the
smallest possible scale is motivated by goals ranging from high-density
information storage to the purposeful transformation of genetic material.
Here we report an atomic-scale modification of the surface of a nearly
perfect germanium crystal, effected by the tungsten tip of a tunnelling
microscope. We believe this to be the smallest spatially controlled,
purposeful transformation yet impressed on matter and we argue that
the limit set by the discreteness of atomic structure has now essentially
been reached.NOTE:Becker's
work on STM-induced atomic manipulation makes use of electric fields
of order 109 Vm-1, not reactive and/or rechargeable
tooltips. The researchers could cause an atomic–scale bump on
a germanium surface using a bias jump with a tungsten tip on a germanium
(111) sample. Tip bias is -1V, tunnel current is 20pA; jump to -4V
and let feedback settle to write. Feature size is 8Å across.
Could not do this on silicon. Success rate varied from >90% to
<10%; seemed better after tip was “recharged” by touching
it to the surface.

In-Whan
Lyo, Phaedon Avouris, “Field-induced
nanometer- to atomic-scale manipulation of silicon surfaces with the
STM,” Science 253(12 July 1991):173-176.ABSTRACT.
The controlled manipulation of silicon at the nanometer scale will
facilitate the fabrication of new types of electronic devices. The
scanning tunneling microscope (STM) can be used to manipulate strongly
bound silicon atoms or clusters at room temperature. Specifically,
by using a combination of electrostatic and chemical forces, surface
atoms can be removed and deposited on the STM tip. The tip can then
move to a predetermined surface site, and the atom or cluster can
be redeposited. The magnitude of such forces and the amount of material
removed can be controlled by applying voltage pulses at different
tip-surface separations.

M.
Aono, A. Kobayashi, F. Grey, H. Uchida, D.H. Huang, “Tip-sample
interactions in the scanning tunneling microscope for atomic-scale
structure fabrication,” J. Appl. Phys.
32(1993):1470-1477; http://adsabs.harvard.edu/abs/1993JaJAP..32.1470A
(abstract)ABSTRACT:
In a scanning tunneling microscope (STM) operated in ultra-high vacuum,
if we place a well-prepared W tip above the Si(111)-7× 7 surface
at a separation of ˜1 nm and apply an appropriate voltage pulse
to it, we can extract a single Si atom from a predetermined position
routinely at room temperature. The extracted Si atoms are redeposited
onto the surface with a certain probability, their positions always
being at a fixed crystallographic site. The redeposited Si atoms can
be displaced intentionally to other crystallographically equivalent
sites. In case of the Si(001)-2× 1 surface, usually two Si atoms
forming a dimer are extracted together. For both surfaces, Si atoms
at crystallographically different sites including step edges are extracted
with different probabilities. The microscopic mechanisms of these
processes are discussed.NOTE: Aono's work
also uses electric fields. This
work demonstrated the ability to pick and place single Si atoms from
Si(111)7x7 and Si(001)2x1 using W tip in UHV with a separation of
about 1 nm when scanning and pulsing, and can routinely remove single
atoms from specific locations. For Si(001), usually two atoms forming
a dimer are removed. The sample is cleaned by flash heatings -- the
tip is etched, electron–bombarded, and then pulsed to clean.
The aparatus can remove single atoms with pulses or can cut grooves
by scanning with raised bias. The whole QID pattern is made in a 50
nm area (no metal, just trenches in Si), with Si ions apparently being
field evaporated from the surface. Polarity does not dominate, but
has some effect due to the difference in critical field for + and
- Si ions. Field strength, not current, causes change (they varied
tunnel current without significant effects). They give the equations
of field evaporation. The center adatoms in Si(111) were more easily
removed. The fraction of atom re–deposition during extraction
varies from negligible to about 19% based on pulse height. It is possible
to move a deposited atom around using other nearby pulses. The deposited/moved
atoms always land at the center of a triangle formed by a corner adatom
and two adjacent center adatoms.

C.T.
Salling, M.G. Lagally, “Fabrication
of atomic-scale structures on Si(001) surfaces,” Science
265(22 July 1994):502-506; http://www.sciencemag.org/cgi/content/abstract/265/5171/502
(abstract)ABSTRACT.
The scanning tunneling microscope has been used to define regular
crystalline structures at room temperature by removing atoms from
the silicon (001) surface. A single atomic layer can be removed to
define features one atom deep and create trenches with ordered floors.
Segments of individual dimer rows can be removed to create structures
with atomically straight edges and with lateral features as small
as one dimer wide. Conditions under which such removal is possible
are defined, and a mechanism is proposed.

Dehuan
Huang, Hironaga Uchida, Masakazu Aono, “Deposition
and subsequent removal of single Si atoms on the Si(111)-7x7 surface
by a scanning tunneling microscope,” J. Vac. Sci.
Technol. B 12(July/August 1994):2429-2433.ABSTRACT.
Single Si atoms can be deposited onto a Si(111)-7x7 sample surface
from the tip of a scanning tunneling microscope, the Si atoms to be
deposited being previously picked up by the tip from another place
on the sample surface. The crystallographic position of these deposited
Si atoms changes as their density increases. The deposited Si atoms
can be re-removed by picking them up again with the tip, the substrate
atomic arrangement remaining unperturbed. It is also possible to fill
Si atom vacancies on the sample surface with a Si atom deposited from
the tip.

Phaedon
Avouris, “Manipulation of matter
at the atomic and molecular levels,” Acc. Chem.
Res. 28(1995):95-102; http://pubs.acs.org/cgi-bin/abstract.cgi/achre4/1995/28/i03/f-pdf/f_ar00051a002.pdf?sessid=6006l3
(first page)EXTRACT.
The “far future” of Feynman began to be realized in the
1980s. Some of the capabilities he dreamed of have been demonstrated,
while others are being developed. Although we are still far from having
a general and reliable “atomic technology”, progress in
the last 15 years or so has been tremendous. Here we describe some
of these developments, starting with the isolation and manipulation
of individual atoms. We then concentrate on atomic and molecular manipulation
using the powerful scanning proximal probe techniques, such as the
scanning tunneling microscope.

Noriaki
Oyabu, Oscar Custance, Insook Yi, Yasuhiro Sugawara, Seizo Morita,
“Mechanical vertical manipulation
of selected single atoms by soft nanoindentation using near contact
atomic force microscopy,” Phys. Rev. Lett.
90(2 May 2003):176102;http://link.aps.org/abstract/PRL/v90/e176102
(Abstract) http://focus.aps.org/story/v11/st19
(APS story)ABSTRACT.
A near contact atomic force microscope operated at low-temperature
is used for vertical manipulation of selected single atoms
from the Si(111)–(7×7) surface. The strong repulsive short-range
chemical force interaction between the closest atoms of both tip apex
and surface during a soft nanoindentation leads to the removal of
a selected silicon atom from its equilibrium position at the surface
without additional perturbation of the (7×7) unit cell. Deposition
of a single atom on a created vacancy at the surface is achieved as
well. These manipulation processes are purely mechanical, since neither
bias voltage nor voltage pulse is applied between probe and sample.
Differences in the mechanical response of the two nonequivalent adatoms
of the Si(111)–(7×7) with the load applied is also detected.NOTE: This landmark
paper is the first to report purely mechanical-based covalent bond-making
and bond-breaking, i.e., the first experimental demonstration of true
vacuum-phase mechanosynthesis.

Morita
S, Sugimoto Y, Oyabu N, Nishi R, Custance O, Sugawara Y, Abe M, “Atom-selective
imaging and mechanical atom manipulation using the non-contact atomic
force microscope,” J. Electron Microsc. (Tokyo)
53(2004):163-168.ABSTRACT.
We succeeded in distinguishing between oxygen and silicon atoms on
an oxygen-adsorbed Si(111)7 x 7 surface, and also distinguished between
silicon and tin atoms on Si(111)7 x 7-Sn intermixed and Si(111) square
root(3) x square root(3)-Sn mosaic-phase surfaces using non-contact
atomic force microscopy (NC-AFM) at room temperature. Atom species
of individual atoms are specified from the number of each atom in
NC-AFM images, the tip-sample distance dependence of NC-AFM images
and/or the surface distribution of each atom. Further, based on the
NC-AFM method but using soft nanoindentation, we achieved two kinds
of mechanical vertical manipulation of individual atoms:
removal of a selected Si adatom and deposition of a Si atom into a
selected Si adatom vacancy on the Si(111)7 x 7 surface at 78 K. Here,
we carefully and slowly indented a Si atom on top of a clean Si tip
apex onto a predetermined Si adatom to remove the targeted Si adatom
and onto a predetermined Si adatom vacancy to deposit a Si atom, i.e.
to repair the targeted Si adatom vacancy. By combining the atom-selective
imaging method with two kinds of mechanical atom manipulation, i.e.
by picking up a selected atom species and by depositing that atom
one by one at the assigned site, we hope to construct nanomaterials
and nanodevices made from more than two kinds of atom species in the
near future.NOTE: This is
another experimental demonstration of true mechanosynthesis, using
silicon (Si) adatoms on Si surface.

N.
Oyabu, O. Custance, M. Abe, S. Morita, “Mechanical
Vertical Manipulation of Single Atoms on the Ge(111)-c(2x8) Surface
by Noncontact Atomic Force Microscopy,” Abstracts of Seventh
International Conference on non-contact Atomic Force Microscopy, Seattle,
Washington, USA, 12-15 September, 2004, p.34;http://www.engr.washington.edu/epp/afm/abstracts/15Oyabu2.pdfABSTRACT.
Recently, noncontact atomic force microscopy was used for performing
controlled mechanical vertical manipulation of selected single atoms
on a surface for the first time. In that work a soft and controlled
nanoindentation of a Si tip on selected positions of the surface was
used for the extraction of single adatoms, as well as for the deposition
of single atoms in a previously created vacancy on the Si(111)-(7x7)
surface. However, those experiments were performed using constant
excitation mode for driving the cantilever oscillation, making the
analysis of the interaction force involved in the vertical manipulation
process difficult. In the present contribution, we report on the mechanical
vertical manipulation of selected single atoms of the Ge(111)-c(2x8)
surface, but using constant amplitude mode. Manipulation
experiments removing single atoms from the surface, and depositing
single atoms coming from the tip in a previously created vacancy on
the Ge(111)-c(2x8) surface using a semiconductor tip will be presented.
To apply the inverse procedure proposed by Giessibl to the frequency
shift vs. tip-surface distance curves associated with the manipulation
processes allows us to obtain information and present a discussion
about the forces before and after the manipulation event, and the
energy dissipated in the process.NOTE: This paper
reports purely mechanical-based covalent bond-making and bond-breaking
(true mechanosynthesis) involving germanium (Ge) atoms on Ge surface.

N.
Oyabu, Y. Sugimoto, M. Abe, O. Custance, S.
Morita, “Lateral manipulation of
single atoms at semiconductor surfaces using atomic force microscopy,”
Nanotechnology 16(2005):S112-S117;http://iopscience.iop.org/0957-4484/16/3/021/
(Abstract)ABSTRACT.
Experimental results on the lateral manipulation of single atoms at
semiconductor surfaces using non-contact atomic force microscopy (NC-AFM)
are presented. These experiments prove that deposited adsorbates on
top of a surface, as well as intrinsic adatoms of semiconductor surfaces,
are suitable for being manipulated using the short-range interaction
force acting between the outermost atoms of a semiconductor tip and
the atoms at the surface. The analysis of the data from some of the
experiments presented here indicates a pulling process of the tip
on the manipulated atoms. The atom-by-atom creation, at room temperature,
of patterns composed by a few inherent atoms of a heterogeneous surface
is also presented.NOTE: The authors
"achieved fully controlled lateral atom manipulation of single
Ge atom adsorbed on a Ge(111)-c(2 × 8) surface at LT (80 K).
In these purely mechanical atom manipulation sessions, at first, they
precisely decreased the tip-sample distance and changed from the noncontact
to the near-contact region, where only a single targeted surface atom
could be mechanically manipulated. For lateral manipulation of adsorbed
single Ge atoms, they found that a tip-sample distance change of ca.
6 pm under 9.3 nm amplitude oscillations, which changed the attractive
force alternately between ca. 0.8 and 1.0 nN, could stably and reproducibly
switch the lateral atom manipulation on and off."

Noriaki
Oyabu, Pablo Pou, Yoshiaki Sugimoto, Pavel Jelinek, Masayuki Abe,
Seizo Morita, Rubén Pérez, Óscar Custance, “Single
Atomic Contact Adhesion and Dissipation in Dynamic Force Microscopy,”
Phys. Rev. Lett. 96(15 March 2006):106101;http://link.aps.org/doi/10.1103/PhysRevLett.96.106101
(Abstract) http://netserver-alt.aip.org/epaps/phys_rev_lett/E-PRLTAO-96-034611/AdditionalInformation.pdf
(paper)ABSTRACT.
By combining dynamic force microscopy experiments and first-principles
calculations, we have studied the adhesion associated with a single
atomic contact between a nanoasperity –
the tip apex–and a semiconductor surface–the Ge(111)-c(2×8). The nanoasperity's
termination has been atomically characterized by extensive comparisons
of the measured short-range force at specific sites with the chemical
forces calculated using many atomic models that vary in structure,
composition, and relative orientation with respect to the surface.
This thorough characterization has allowed us to explain the dissipation
signal observed in atomic-resolution images and force spectroscopic
measurements, as well as to identify a dissipation channel and the
associated atomic processes.

Sugimoto
Y, Pou P, Abe M, Jelinek P, Perez R, Morita S, Custance O, “Chemical
identification of individual surface atoms by atomic force microscopy,”
Nature 446(1 March 2007):64-67.ABSTRACT.
Scanning probe microscopy is a versatile and powerful method that
uses sharp tips to image, measure and manipulate matter at surfaces
with atomic resolution. At cryogenic temperatures, scanning probe
microscopy can even provide electron tunnelling spectra that serve
as fingerprints of the vibrational properties of adsorbed molecules
and of the electronic properties of magnetic impurity atoms, thereby
allowing chemical identification. But in many instances, and particularly
for insulating systems, determining the exact chemical composition
of surfaces or nanostructures remains a considerable challenge. In
principle, dynamic force microscopy should make it possible to overcome
this problem: it can image insulator, semiconductor and metal surfaces
with true atomic resolution, by detecting and precisely measuring
the short-range forces that arise with the onset of chemical bonding
between the tip and surface atoms and that depend sensitively on the
chemical identity of the atoms involved. Here we report precise measurements
of such short-range chemical forces, and show that their dependence
on the force microscope tip used can be overcome through a normalization
procedure. This allows us to use the chemical force measurements as
the basis for atomic recognition, even at room temperature. We illustrate
the performance of this approach by imaging the surface of a particularly
challenging alloy system and successfully identifying the three constituent
atomic species silicon, tin and lead, even though these exhibit very
similar chemical properties and identical surface position preferences
that render any discrimination attempt based on topographic measurements
impossible.

Sugimoto
Y, Jelinek P, Pou P, Abe M, Morita S, Perez R, Custance O, “Mechanism
for room-temperature single-atom lateral manipulations on semiconductors
using dynamic force microscopy,” Phys. Rev. Lett.
98(9 March 2007):106104.ABSTRACT.
Vacancy-mediated lateral manipulations of intrinsic adatoms of the
Si(111)-(7x7) surface at room temperature are reported. The topographic
signal during the manipulation combined with force spectroscopy measurements
reveals that these manipulations can be ascribed to the so-called
pulling mode, and that the Si adatoms were manipulated in the attractive
tip-surface interaction regime at the relatively low short-range force
value associated to the manipulation set point. First-principles calculations
reveal that the presence of the tip induces structural relaxations
that weaken the adatom surface bonds and manifests in a considerable
local reduction of the natural diffusion barriers to adjacent adsorption
positions. Close to the short-range forces measured in the experiments,
these barriers are lowered near the limit that enables a thermally
activated hopping at room temperature.

Yoshiaki
Sugimoto, Pablo Pou, Oscar Custance, Pavel Jelinek, Masayuki Abe,
Ruben Perez, Seizo Morita, “Complex
Patterning by Vertical Interchange Atom Manipulation Using Atomic
Force Microscopy,” Science 322(17 October 2008):413-417;http://www.sciencemag.org/cgi/content/full/322/5900/413
(paper) http://www.sciencemag.org/cgi/content/full/322/5900/413/DC1
(supplement)ABSTRACT.
The ability to incorporate individual atoms in a surface following
predetermined arrangements may bring future atom-based technological
enterprises closer to reality. Here, we report the assembling of complex
atomic patterns at room temperature by the vertical interchange of
atoms between the tip apex of an atomic force microscope and a semiconductor
surface. At variance with previous methods, these manipulations were
produced by exploring the repulsive part of the short-range chemical
interaction between the closest tip-surface atoms. By using first-principles
calculations, we clarified the basic mechanisms behind the vertical
interchange of atoms, characterizing the key atomistic processes involved
and estimating the magnitude of the energy barriers between the relevant
atomic configurations that leads to these manipulations.NOTE: This paper
reports purely mechanical-based covalent bond-making and bond-breaking
(true vacuum-phase mechanosynthesis) involving atom by atom substitution
of silicon (Si) atoms for tin (Sn) atoms in an Sn monolayer surface
on a Si(111) surface; also demonstrates atomically precise exchange
of lead (Pb) and indium (In) on Si(111) surface. This is the first
report of a complex pattern being drawn on a 2D surface, literally
atom by atom, purely via mechanical forces.

Other
DMS Tool and Related Studies (Theory)

Ralph
C. Merkle, “A proposed
‘metabolism’ for a hydrocarbon assembler,” Nanotechnology
8(1997):149-162;http://www.zyvex.com/nanotech/hydroCarbonMetabolism.htmlABSTRACT.
Molecular manufacturing should let us synthesize most arrangements
of atoms that are consistent with physical law. Assemblers have been
proposed as a means for accomplishing this objective. They would be
able to build a wide range of useful products as well as copies of
themselves. A simpler though less general proposal is a hydrocarbon
assembler, restricted to manufacturing relatively stiff hydrocarbons.
The design and analysis of such an assembler should be substantially
simpler than that of a more general assembler. In this paper, we consider
the "intermediary metabolism" of a hydrocarbon assembler,
i.e., the set of reactions that permit processing of the feedstock
molecules and their conversion into molecular tools (positionally
controlled carbenes, radicals, and other reactive species). The specific
feedstock molecule analyzed is butadiyne (a linear molecule, C4H2,
also known as diacetylene; not to be confused with the more common
but chemically distinct non-linear molecule butadiene: C4H6).

Fu-He
Wang, Jin-Long Yang, Jia-Ming Li, “Theoretical
study of single-atom extraction using STM,” Phys.
Rev. B 59(1999):16053–16060;http://prb.aps.org/abstract/PRB/v59/i24/p16053_1ABSTRACT.
Based on the discrete variational method with the local-density-functional
approximation, we chose cluster models to simulate the extraction
of a single Al atom from Al(111) sample surface by a scanning-tunneling
microscopy W tip with and without external bias voltages. Our cluster
calculations, which can deal with the detailed geometry of the sample
and the tip (especially with an active site), can provide useful and
relatively reliable results: (1) The “chemical interactions”
between the sample and the tip play an important role in single-atom
extraction processes; e.g., an Al atom can be extracted as the tip-sample
separation becomes 10 a.u. (5.3 Å) without any external fields.
(2) The polarity and the value of the external bias (near the threshold)
are other important factors; e.g., at the tip-sample separation 12
a.u., an Al atom can be extracted with the threshold field (0.6 V/Å,
positive bias to the sample), and the extracted Al atom can be put
back with a negative bias to the sample. (3) The W atom on the tip
cannot be extracted. NOTE: This is the first proposed
purely mechanosynthetic aluminum extraction tool.
.

Robert
A. Freitas Jr., Ralph C. Merkle, “A
Minimal Toolset for Positional Diamond Mechanosynthesis,”
J. Comput. Theor. Nanosci. 5(May 2008):760-861;
http://www.MolecularAssembler.com/Papers/MinToolset.pdfABSTRACT.
This paper presents the first theoretical quantitative systems level
study of a complete suite of reaction pathways for scanning-probe
based ultrahigh-vacuum diamond mechanosynthesis (DMS). A minimal toolset
is proposed for positionally controlled DMS consisting of three primary
tools – the (1) Hydrogen Abstraction (HAbst), (2) Hydrogen Donation
(HDon), and (3) Dimer Placement (DimerP) tools – and six auxiliary
tools – the (4) Adamantane radical (AdamRad) and (5) Germyladamantane
radical (GeRad) handles, the (6) Methylene (Meth), (7) Germylmethylene
(GM), and (8) Germylene (Germ) tools, and (9) the Hydrogen Transfer
(HTrans) tool which is a simple compound of two existing tools (HAbst+GeRad).
Our description of this toolset, the first to exhibit 100% process
closure, explicitly specifies all reaction steps and reaction pathologies,
also for the first time. The toolset employs three element types (C,
Ge, and H) and requires inputs of four feedstock molecules –
CH4 and C2H2 as carbon sources, Ge2H6
as the germanium source, and H2 as a hydrogen source. The
present work shows that the 9-tooltype toolset can, using only these
simple bulk-produced chemical inputs: (1) fabricate all nine tooltypes,
including their adamantane handle structures and reactive tool intermediates,
starting from a flat passivated diamond surface or an adamantane seed
structure; (2) recharge all nine tooltypes after use; and (3) build
both clean and hydrogenated molecularly-precise unstrained cubic diamond
C(111)/C(110)/C(100) and hexagonal diamond surfaces of process-unlimited
size, including some Ge-substituted variants; methylated and ethylated
surface structures; handled polyyne, polyacetylene and polyethylene
chains of process-unlimited length; and both flat graphene sheet and
curved graphene nanotubes. Reaction pathways and transition geometries
involving 1620 tooltip/workpiece structures were analyzed using Density
Functional Theory (DFT) in Gaussian 98 at the B3LYP/6-311+G(2d,p)
// B3LYP/3-21G* level of theory to compile 65 Reaction Sequences comprised
of 328 reaction steps, 354 unique pathological side reactions and
1321 reported DFT energies. The reactions should exhibit high reliability
at 80 K and moderate reliability at 300 K. This toolset provides clear
developmental targets for a comprehensive near-term DMS implementation
program.NOTE: First paper
to propose a complete set of atomically precise mechanosynthetic reactions
for building diamond. See also video
presentation.

Denis
Tarasov, Natalia Akberova, Ekaterina Izotova, Diana Alisheva, Maksim
Astafiev, Robert A. Freitas Jr., “Optimal
Tooltip Trajectories in a Hydrogen Abstraction Tool Recharge Reaction
Sequence for Positionally Controlled Diamond Mechanosynthesis,”J. Comput. Theor. Nanosci.
7(February 2010):325-353;http://www.molecularassembler.com/Papers/TarasovFeb2010.pdfABSTRACT.
The use of precisely applied mechanical forces to induce site-specific
chemical transformations is called positional mechanosynthesis, and
diamond is an important early target for achieving mechanosynthesis
experimentally. A key step in diamond mechanosynthesis (DMS) employs
an ethynyl-based hydrogen abstraction tool (HAbst) for the site-specific
mechanical dehydrogenation of H-passivated diamond surfaces, creating
an isolated radical site that can accept adatoms via radical-radical
coupling in a subsequent positionally controlled reaction step. The
abstraction tool, once used (HAbstH), must be recharged by removing
the abstracted hydrogen atom from the tooltip, before the tool can
be used again. This paper presents the first theoretical study of
DMS tool-workpiece operating envelopes and optimal tooltip trajectories
for any positionally controlled reaction sequence – and more
specifically, one that may be used to recharge a spent hydrogen abstraction
tool – during scanning-probe based ultrahigh-vacuum diamond
mechanosynthesis. Trajectories were analyzed using Density Functional
Theory (DFT) in PC-GAMESS at the B3LYP/6-311G(d,p) // B3LYP/3-21G(2d,p)
level of theory. The results of this study help to define equipment
and tooltip motion requirements that may be needed to execute the
proposed reaction sequence experimentally and provide support for
early developmental targets as part of a comprehensive near-term DMS
implementation program.NOTE: First published
theoretical study of DMS tool-workpiece operating envelopes and optimal
tooltip trajectories for a complete positionally controlled reaction
sequence.

Denis
Tarasov, Ekaterina Izotova, Diana Alisheva, Natalia Akberova, Robert
A. Freitas Jr., “Structural Stability
of Clean and Passivated Nanodiamonds having Ledge, Step, or Corner
Features,”J. Comput.
Theor. Nanosci. 9(January 2012):144-158; http://www.molecularassembler.com/Papers/TarasovFeb2012.pdfABSTRACT.
The use of precisely applied mechanical forces to induce site-specific
chemical transformations is called positional mechanosynthesis, and
diamond is an important early target for achieving mechanosynthesis
experimentally. The next major experimental milestone may be the mechanosynthetic
fabrication of atomically precise 3D structures, creating readily
accessible diamond-based nanomechanical components engineered to form
desired architectures possessing superlative mechanical strength,
stiffness, and strength-to-weight ratio. To help motivate this future
experimental work, the present paper addresses the basic stability
of nanoscale diamond structures with clean or hydrogenated surfaces
that possess certain simple features including ledges, steps, and
corners. Computational studies using Density Functional Theory (DFT)
with the Car-Parrinello Molecular Dynamics (CPMD) code, consuming
~2,284,108.97 CPU-hours of runtime on the IBM Blue Gene/P supercomputer
(23 TFlops), confirm that fully hydrogenated nanodiamonds 1-2 nm in
size possessing ledges with various combinations of convex or concave
edgelines where any two of the three principal diamond faces meet
will maintain stable sp3 hybridization.

Denis
Tarasov, Ekaterina Izotova, Diana Alisheva, Natalia Akberova, Robert
A. Freitas Jr., “Optimal Approach
Trajectories for a Hydrogen Donation Tool in Positionally Controlled
Diamond Mechanosynthesis,”J.
Comput. Theor. Nanosci. 10(September 2013):1899-1907;
http://www.molecularassembler.com/Papers/TarasovSep2013.pdfABSTRACT.
The use of precisely applied mechanical forces to induce site-specific
chemical transformations is called positional mechanosynthesis, and
diamond is an important early target for achieving mechanosynthesis
experimentally. A key step in diamond mechanosynthesis (DMS) may employ
a Ge-substituted adamantane-based hydrogen donation tool (HDon) for
the site-specific mechanical hydrogenation of depassivated diamond
surfaces. This paper presents the first theoretical study of DMS tool-workpiece
operating envelopes and optimal tool approach trajectories for a positionally
controlled hydrogen donation tool during scanning-probe based UHV
diamond mechanosynthesis. Trajectories were analyzed using Density
Functional Theory (DFT) in PC-GAMESS at the B3LYP/6-311G(d,p) // B3LYP/3-21G(2d,p)
level of theory. The results of this study help to define equipment
and tooltip motion requirements that may be needed to execute the
proposed reaction sequence experimentally and provide support for
early developmental targets as part of a comprehensive near-term DMS
implementation program.

Other
DMS Tool and Related Studies
(Experimental)

No entries.

Other
Molecular Manufacturing Related Studies

Bryan
W. Wagner, Thomas P. Way, “MolML:
An abstract scripting language for assembly of mechnical nanocomputer
architectures,” 2006 International Conference on Computing in
Nanotechnology (CNAN'06), 2006; http://www.csc.villanova.edu/~tway/publications/wagnerCNAN06.pdfABSTRACT.
Sizes of computer components are reaching nanoscale dimensions, causing
physical limitations to be met in traditional computer architectures.
This study surveys the field of alternative nanocomputer architectures,
including the nano-mechanical computational machines first proposed
by Eric Drexler. A high-level XML programming language, MolML, is
introduced as a scripting language for hydrocarbon assembly of mechanical
nanocomputers.

Thomas
P. Way, Tao Tao, “Compiling a Mechanical
Nanocomputer Adder,” International Conference on Computer Design,
2007; http://www.csc.villanova.edu/~tway/publications/wayCDES07.pdfABSTRACT.
Computer component fabrication is approaching physical limits of traditional
photolithographic fabrication techniques. An alternative computer
architecture may be enabled by the rapidly maturing field of nanotechnology,
and consist of nanomechanical computational machines similar to those
first proposed by Eric Drexler, or other nanoscale components. In
this study, we propose the design of a nanocompiler which targets
a simulated hydrocarbon assembler. The compiler framework and resulting
nano-mechanical machine is simulated using a component-level Colored
Petri Net model of a 32-bit adder and an atomic-level gate simulator.
Future work is proposed to extend the framework to simulate a full
range nano-mechanical processing components.

Andres
Jaramillo-Botero, “Molecular manipulator:
Dynamic Design Criteria,” Dekker Encyclopedia of Nanoscience
and Nanotechnology, Second Edition, 2009; http://www.tandfonline.com/doi/abs/10.1081/E-ENN2-120024165
(abstract)ABSTRACT.
The ability to intentionally manipulate three-dimensional (3-D) irregular-shaped
matter with atomic precision, abiding to physical laws, is considered
as one of the ultimate goals of nanoscience and engineering. Nature
has given us a vast assortment of biological molecular machines that
demonstrate the viability of this goal, including, among others, the
ribosome (which can translate mRNA instructions into proteins) and
kinesin, an enzyme that acts as a molecular motor which pulls things
toward the outer reaches of the cell. In nerve cells, it is kinesin
that pulls vesicles or other cellular materials from the cell body
to the nerve endings. These biological systems are primarily “application-specific
molecular machines.” They are not universal assemblers that
could, in principle, be used in a programmable fashion to perform
alternate functions at the molecular level. Self-replicating programmable
manufacturing systems able to arrange atoms for multiple “applications”
would require a universal assembler with an appropriate end-effector
and a corresponding controller. The scope of this entry explores design
criteria for such a universal assembler. This
article reviews the literature on the creation of nanometer-scale
spatial positioners, from a kinematic and dynamic standpoint, as one
of the basic building blocks for an atomic-scale manipulator (to arrange
differently functionalized molecular building blocks into a lattice
or any other nanometer-scale object in a specified and complex pattern,
it is necessary to introduce positional control). The development
of theoretical criteria for the design of reduced constrained dynamic
complexity of a nanoscale positioning device (nanomanipulator), based
on the equations of motion (EOM) for spatial serially articulated
rigid multibodies, is presented in this article. By using a rigid-body
semiclassical mechanics approach, it is shown how dynamic complexities,
such as coupling and nonlinearities introduced by high-speed operation,
complicate the control task and deteriorate performance. The first
section of the article introduces the reader to appropriate state
space forms of the EOM for a serially coupled set of rigid bodies
using internal coordinates. This allows a compact mathematical description
of the problem at hand and exposes the intended solution by permitting
concise physical insight. The second section develops the complete
set of EOM for both the Newton–Euler and Lagrange–Euler
formulations. From the state space equivalence of both methods, the
EOM are then expressed as a function of the articulated body inertia
operator for the multibody, leading to a highly dependent form of
the EOM on this operator. The internal matrix structure of the articulated
body inertia is then revealed. The third section presents the analysis
that leads to a reduced set of EOM from the structural simplification
of the articulated body inertia matrix and develops the general kinematics
and mass distribution criteria for doing so. From the resulting analysis,
a set of compliant manipulator configurations that could, in principle,
be built from carbon nanotubes, linked by direct-driven rotational
molecular joints, is shown. Finally, the last section concludes on
the obtained results and describes current and future work.

Robert
Bogue, “Nanoscale fabrication:
techniques, limitations and future prospects,” Assembly Automation
31(2011):304-308; http://www.ingentaconnect.com/content/mcb/033/2011/00000031/00000004/art00001
(abstract)ABSTRACT.
Purpose - This paper aims to provide an overview of the strategies
and techniques being used and developed for the fabrication of nanoscale
devices. Design/methodology/approach - This paper discusses various
nanofabrication technologies and strategies and highlights their merits
and limitations. It concludes with a consideration of longer-term
possibilities. Findings - It is shown that top-down nanofabrication
frequently uses lithographic and other techniques derived from the
microtechnology industry but recent research appears to have identified
a limit to its capabilities. Bottom-up nanofabrication is less well-developed
but techniques such as molecular mechanosynthesis may offer unique
capabilities in the longer-term. Originality/value - The paper provides
a timely review of the rapidly developing field of nanofabrication
technology.